I: pbuilder: network access will be disabled during build I: Current time: Tue Feb 11 14:20:58 +14 2025 I: pbuilder-time-stamp: 1739233258 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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_202009.4-1.dsc] I: copying [./rdkit_202009.4.orig.tar.xz] I: copying [./rdkit_202009.4-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.hFIwLIQd/trustedkeys.kbx': General error gpgv: Signature made Sun Feb 21 10:42:16 2021 gpgv: using RSA key 9CA877749FAB2E4FA96862ECDC686A27B43481B0 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rdkit_202009.4-1.dsc dpkg-source: info: extracting rdkit in rdkit-202009.4 dpkg-source: info: unpacking rdkit_202009.4.orig.tar.xz dpkg-source: info: unpacking rdkit_202009.4-1.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 postgres_disable_failing_tests.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 postgres_compile_fixes.patch dpkg-source: info: applying sphinx_compile_fixes.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/110048/tmp/hooks/D01_modify_environment starting debug: Running on ionos16-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 Feb 11 00:21 /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/110048/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/110048/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.1.4(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,-fixfilepath parallel=15 ' DIRSTACK=() DISTRIBUTION=bullseye EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=52000718388d4aa2b81073f87fd3d958 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=110048 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.66C3z6rs/pbuilderrc_72KE --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.66C3z6rs/b2 --logfile b2/build.log rdkit_202009.4-1.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://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Mar 27 2022 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 7 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 7 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 71928 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 Jan 25 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 Nov 7 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Jan 20 2022 more -rwsr-xr-x 1 root root 50720 Jan 20 2022 mount -rwxr-xr-x 1 root root 13856 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 7 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 9 Feb 11 00:21 sh -> /bin/bash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Jan 20 2022 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Jan 20 2022 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 7 2019 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 5898 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 8049 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/110048/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 (>> 9), dh-python, doxygen, flex, imagemagick, latexmk, libboost-dev, libboost-iostreams-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-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, 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 ... 17763 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 (>> 9); however: Package debhelper 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 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 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-11{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} lib64atomic1{a} lib64gcc-s1{a} lib64stdc++6{a} libaom0{a} libapache-pom-java{a} libarchive-zip-perl{a} libarchive13{a} libblas3{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} libc6-amd64{a} libcairo-gobject2{a} libcairo2{a} libclang-common-11-dev{a} libclang-cpp11{a} libclang1-11{a} libcmark-gfm-extensions0{a} libcmark-gfm0{a} libcommons-logging-java{a} libcommons-parent-java{a} libcoordgen-dev{a} libcoordgen1{a} libcurl4{a} libdatrie1{a} libdav1d4{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} libfontconfig1{a} libfreetype-dev{a} libfreetype6{a} libfreetype6-dev{a} libfribidi0{a} libgc1{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libheif1{a} libice6{a} libicu-dev{a} libicu67{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp24{a} libkpathsea6{a} liblapack3{a} liblcms2-2{a} libldap-2.4-2{a} libllvm11{a} liblqr-1-0{a} libltdl7{a} libmaeparser-dev{a} libmaeparser1{a} libmagic-mgc{a} libmagic1{a} libmagickcore-6.q16-6{a} libmagickwand-6.q16-6{a} libmd0{a} libmpdec3{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnuma1{a} libobjc-10-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} libpdfbox-java{a} libpfm4{a} libpipeline1{a} libpixman-1-0{a} libpng-dev{a} libpng16-16{a} libpq-dev{a} libpq5{a} libprocps8{a} libpsl5{a} libptexenc1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.9{a} libpython3.9-dev{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librhash0{a} librsvg2-2{a} librsvg2-bin{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsm6{a} libsqlite3-dev{a} libssh2-1{a} libsub-override-perl{a} libsynctex2{a} libteckit0{a} libtexlua53{a} libtexluajit2{a} libthai-data{a} libthai0{a} libtiff5{a} libtinfo-dev{a} libtool{a} libuchardet0{a} libuv1{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx265-192{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} libyaml-0-2{a} libz3-4{a} libz3-dev{a} libzzip-0-13{a} llvm-11{a} llvm-11-dev{a} llvm-11-runtime{a} llvm-11-tools{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} netbase{a} openssl{a} pandoc{a} pandoc-data{a} pkg-config{a} po-debconf{a} postgresql-client-13{a} postgresql-client-common{a} postgresql-common{a} postgresql-server-dev-13{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-commonmark{a} python3-dateutil{a} python3-dev{a} python3-distutils{a} python3-docutils{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-pyparsing{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} python3.9{a} python3.9-dev{a} python3.9-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} 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} x11-common{a} xdg-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: atril binfmt-support curl dvisvgm e2fsprogs evince ghostscript gsfonts gv javascript-common libarchive-cpio-perl libfile-mimeinfo-perl libfl-dev libgdk-pixbuf2.0-bin libglib2.0-data libgpm2 libldap-common libltdl-dev libmagickcore-6.q16-6-extra libmail-sendmail-perl libnet-dbus-perl libomp-11-dev libpng-tools librsvg2-common libsasl2-modules 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 python3-xlwt qpdfview qpdfview-ps-plugin ruby tex-gyre 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, 291 newly installed, 0 to remove and 0 not upgraded. Need to get 317 MB of archives. After unpacking 1521 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-8+deb11u1 [149 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 flex i386 2.6.4-8 [434 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 libfftw3-double3 i386 3.3.8-2 [640 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2+deb11u5 [101 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 libpng16-16 i386 1.6.37-3 [303 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 libfreetype6 i386 2.10.4+dfsg-1+deb11u1 [430 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 ucf all 3.0043 [74.0 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libfontconfig1 i386 2.13.1-4.2 [358 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 libaom0 i386 1.0.0.errata1-3+deb11u1 [1150 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libdav1d4 i386 0.7.1-3 [262 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libde265-0 i386 1.0.11-0+deb11u1 [189 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libnuma1 i386 2.0.12-1+b1 [27.9 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libx265-192 i386 3.4-2 [668 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 libheif1 i386 1.11.0-1 [208 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 libjbig0 i386 2.1-3.1+b2 [31.5 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo i386 1:2.0.6-4 [160 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 liblcms2-2 i386 2.12~rc1-2 [161 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 libglib2.0-0 i386 2.66.8-1 [1437 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 liblqr-1-0 i386 0.4.2-2.1 [30.6 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 libltdl7 i386 2.4.6-15 [392 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 libopenjp2-7 i386 2.4.0-3 [179 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libwebp6 i386 0.6.1-2.1+deb11u2 [269 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libtiff5 i386 4.2.0-1+deb11u4 [305 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 libwebpdemux2 i386 0.6.1-2.1+deb11u2 [88.2 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libwebpmux3 i386 0.6.1-2.1+deb11u2 [99.0 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1+deb11u1 [111 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libxcb1 i386 1.14-3 [144 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 libx11-data all 2:1.7.2-1+deb11u1 [311 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libx11-6 i386 2:1.7.2-1+deb11u1 [796 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 libxext6 i386 2:1.3.3-1.1 [55.2 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7+deb11u4 [728 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 imagemagick-6-common all 8:6.9.11.60+dfsg-1.3+deb11u1 [211 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 libmagickcore-6.q16-6 i386 8:6.9.11.60+dfsg-1.3+deb11u1 [1877 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libmagickwand-6.q16-6 i386 8:6.9.11.60+dfsg-1.3+deb11u1 [437 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 mailcap all 3.69 [31.7 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 mime-support all 3.66 [10.9 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 tzdata all 2021a-1+deb11u10 [286 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 sgml-base all 1.30 [15.1 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 tex-common all 6.16 [53.7 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 netbase all 6.3 [19.9 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 libncurses6 i386 6.2+20201114-2+deb11u2 [110 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libprocps8 i386 2:3.3.17-5 [64.2 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 procps i386 2:3.3.17-5 [501 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 openssl i386 1.1.1w-0+deb11u1 [869 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 ca-certificates all 20210119 [158 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3+deb11u1 [273 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3+deb11u1 [135 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3+deb11u1 [69.2 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 78 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 80 http://deb.debian.org/debian bullseye/main i386 bison i386 2:3.7.5+dfsg-1 [1114 kB] Get: 81 http://deb.debian.org/debian bullseye/main i386 catch2 i386 2.13.4-2 [478 kB] Get: 82 http://deb.debian.org/debian bullseye/main i386 libedit2 i386 3.1-20191231-2+b1 [101 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 libz3-4 i386 4.8.10-1 [7737 kB] Get: 84 http://deb.debian.org/debian bullseye/main i386 libllvm11 i386 1:11.0.1-2 [17.7 MB] Get: 85 http://deb.debian.org/debian bullseye/main i386 libclang-cpp11 i386 1:11.0.1-2 [9562 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 libgc1 i386 1:8.0.4-3 [242 kB] Get: 87 http://deb.debian.org/debian bullseye/main i386 libobjc4 i386 10.2.1-6 [45.0 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 libobjc-10-dev i386 10.2.1-6 [163 kB] Get: 89 http://deb.debian.org/debian bullseye/main i386 libc6-amd64 i386 2.31-13+deb11u6 [2682 kB] Get: 90 http://deb.debian.org/debian bullseye/main i386 lib64atomic1 i386 10.2.1-6 [8992 B] Get: 91 http://deb.debian.org/debian bullseye/main i386 lib64gcc-s1 i386 10.2.1-6 [41.2 kB] Get: 92 http://deb.debian.org/debian bullseye/main i386 lib64stdc++6 i386 10.2.1-6 [476 kB] Get: 93 http://deb.debian.org/debian bullseye/main i386 libclang-common-11-dev i386 1:11.0.1-2 [4844 kB] Get: 94 http://deb.debian.org/debian bullseye/main i386 libclang1-11 i386 1:11.0.1-2 [5429 kB] Get: 95 http://deb.debian.org/debian bullseye/main i386 clang-11 i386 1:11.0.1-2 [109 kB] Get: 96 http://deb.debian.org/debian bullseye/main i386 cmake-data all 3.18.4-2+deb11u1 [1725 kB] Get: 97 http://deb.debian.org/debian bullseye/main i386 libarchive13 i386 3.4.3-2+deb11u1 [384 kB] Get: 98 http://deb.debian.org/debian bullseye/main i386 libsasl2-modules-db i386 2.1.27+dfsg-2.1+deb11u1 [70.1 kB] Get: 99 http://deb.debian.org/debian bullseye/main i386 libsasl2-2 i386 2.1.27+dfsg-2.1+deb11u1 [110 kB] Get: 100 http://deb.debian.org/debian bullseye/main i386 libldap-2.4-2 i386 2.4.57+dfsg-3+deb11u1 [244 kB] Get: 101 http://deb.debian.org/debian bullseye/main i386 libnghttp2-14 i386 1.43.0-1 [85.7 kB] Get: 102 http://deb.debian.org/debian bullseye/main i386 libpsl5 i386 0.21.0-1.2 [57.9 kB] Get: 103 http://deb.debian.org/debian bullseye/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 104 http://deb.debian.org/debian bullseye/main i386 libssh2-1 i386 1.9.0-2 [164 kB] Get: 105 http://deb.debian.org/debian bullseye/main i386 libcurl4 i386 7.74.0-1.3+deb11u9 [377 kB] Get: 106 http://deb.debian.org/debian bullseye/main i386 libjsoncpp24 i386 1.9.4-4 [86.1 kB] Get: 107 http://deb.debian.org/debian bullseye/main i386 librhash0 i386 1.4.1-2 [144 kB] Get: 108 http://deb.debian.org/debian bullseye/main i386 libuv1 i386 1.40.0-2 [139 kB] Get: 109 http://deb.debian.org/debian bullseye/main i386 cmake i386 3.18.4-2+deb11u1 [7029 kB] Get: 110 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 111 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 112 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 113 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 114 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 115 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 116 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 117 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 118 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 119 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 120 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 121 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 122 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 123 http://deb.debian.org/debian bullseye/main i386 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 124 http://deb.debian.org/debian bullseye/main i386 python3-distutils all 3.9.2-1 [143 kB] Get: 125 http://deb.debian.org/debian bullseye/main i386 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 126 http://deb.debian.org/debian bullseye/main i386 xml-core all 0.18+nmu1 [23.8 kB] Get: 127 http://deb.debian.org/debian bullseye/main i386 docutils-common all 0.16+dfsg-4 [129 kB] Get: 128 http://deb.debian.org/debian bullseye/main i386 doxygen i386 1.9.1-1 [4426 kB] Get: 129 http://deb.debian.org/debian bullseye/main i386 fontconfig i386 2.13.1-4.2 [417 kB] Get: 130 http://deb.debian.org/debian bullseye/main i386 fonts-lmodern all 2.004.5-6.1 [4540 kB] Get: 131 http://deb.debian.org/debian bullseye/main i386 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 132 http://deb.debian.org/debian bullseye/main i386 icu-devtools i386 67.1-7 [209 kB] Get: 133 http://deb.debian.org/debian bullseye/main i386 imagemagick-6.q16 i386 8:6.9.11.60+dfsg-1.3+deb11u1 [383 kB] Get: 134 http://deb.debian.org/debian bullseye/main i386 imagemagick i386 8:6.9.11.60+dfsg-1.3+deb11u1 [166 kB] Get: 135 http://deb.debian.org/debian bullseye/main i386 libpaper1 i386 1.1.28+b1 [21.7 kB] Get: 136 http://deb.debian.org/debian bullseye/main i386 libpaper-utils i386 1.1.28+b1 [18.6 kB] Get: 137 http://deb.debian.org/debian bullseye/main i386 libkpathsea6 i386 2020.20200327.54578-7+deb11u1 [176 kB] Get: 138 http://deb.debian.org/debian bullseye/main i386 libptexenc1 i386 2020.20200327.54578-7+deb11u1 [65.2 kB] Get: 139 http://deb.debian.org/debian bullseye/main i386 libsynctex2 i386 2020.20200327.54578-7+deb11u1 [86.1 kB] Get: 140 http://deb.debian.org/debian bullseye/main i386 libtexlua53 i386 2020.20200327.54578-7+deb11u1 [146 kB] Get: 141 http://deb.debian.org/debian bullseye/main i386 libtexluajit2 i386 2020.20200327.54578-7+deb11u1 [284 kB] Get: 142 http://deb.debian.org/debian bullseye/main i386 t1utils i386 1.41-4 [62.3 kB] Get: 143 http://deb.debian.org/debian bullseye/main i386 libpixman-1-0 i386 0.40.0-1.1~deb11u1 [545 kB] Get: 144 http://deb.debian.org/debian bullseye/main i386 libxcb-render0 i386 1.14-3 [112 kB] Get: 145 http://deb.debian.org/debian bullseye/main i386 libxcb-shm0 i386 1.14-3 [102 kB] Get: 146 http://deb.debian.org/debian bullseye/main i386 libxrender1 i386 1:0.9.10-1 [34.1 kB] Get: 147 http://deb.debian.org/debian bullseye/main i386 libcairo2 i386 1.16.0-5 [746 kB] Get: 148 http://deb.debian.org/debian bullseye/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB] Get: 149 http://deb.debian.org/debian bullseye/main i386 libharfbuzz0b i386 2.7.4-1 [1490 kB] Get: 150 http://deb.debian.org/debian bullseye/main i386 libteckit0 i386 2.5.10+ds1-3 [277 kB] Get: 151 http://deb.debian.org/debian bullseye/main i386 x11-common all 1:7.7+22 [252 kB] Get: 152 http://deb.debian.org/debian bullseye/main i386 libice6 i386 2:1.0.10-1 [60.8 kB] Get: 153 http://deb.debian.org/debian bullseye/main i386 libsm6 i386 2:1.2.3-1 [35.7 kB] Get: 154 http://deb.debian.org/debian bullseye/main i386 libxt6 i386 1:1.2.0-1 [195 kB] Get: 155 http://deb.debian.org/debian bullseye/main i386 libxmu6 i386 2:1.1.2-2+b3 [62.8 kB] Get: 156 http://deb.debian.org/debian bullseye/main i386 libxpm4 i386 1:3.5.12-1.1~deb11u1 [51.2 kB] Get: 157 http://deb.debian.org/debian bullseye/main i386 libxaw7 i386 2:1.0.13-1.1 [210 kB] Get: 158 http://deb.debian.org/debian bullseye/main i386 libxi6 i386 2:1.7.10-1 [85.1 kB] Get: 159 http://deb.debian.org/debian bullseye/main i386 libzzip-0-13 i386 0.13.62-3.3+deb11u1 [57.7 kB] Get: 160 http://deb.debian.org/debian bullseye/main i386 texlive-binaries i386 2020.20200327.54578-7+deb11u1 [10.1 MB] Get: 161 http://deb.debian.org/debian bullseye/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 162 http://deb.debian.org/debian bullseye/main i386 texlive-base all 2020.20210202-3 [20.8 MB] Get: 163 http://deb.debian.org/debian bullseye/main i386 texlive-latex-base all 2020.20210202-3 [1120 kB] Get: 164 http://deb.debian.org/debian bullseye/main i386 latexmk all 1:4.70b-0.2 [407 kB] Get: 165 http://deb.debian.org/debian bullseye/main i386 libapache-pom-java all 18-1 [4676 B] Get: 166 http://deb.debian.org/debian bullseye/main i386 libblas3 i386 3.9.0-3+deb11u1 [147 kB] Get: 167 http://deb.debian.org/debian bullseye/main i386 libboost1.74-dev i386 1.74.0-9 [9534 kB] Get: 168 http://deb.debian.org/debian bullseye/main i386 libboost-atomic1.74.0 i386 1.74.0-9 [244 kB] Get: 169 http://deb.debian.org/debian bullseye/main i386 libboost-atomic1.74-dev i386 1.74.0-9 [245 kB] Get: 170 http://deb.debian.org/debian bullseye/main i386 libboost-chrono1.74.0 i386 1.74.0-9 [254 kB] Get: 171 http://deb.debian.org/debian bullseye/main i386 libboost-chrono1.74-dev i386 1.74.0-9 [262 kB] Get: 172 http://deb.debian.org/debian bullseye/main i386 libboost-date-time1.74.0 i386 1.74.0-9 [241 kB] Get: 173 http://deb.debian.org/debian bullseye/main i386 libboost-serialization1.74.0 i386 1.74.0-9 [346 kB] Get: 174 http://deb.debian.org/debian bullseye/main i386 libboost-serialization1.74-dev i386 1.74.0-9 [390 kB] Get: 175 http://deb.debian.org/debian bullseye/main i386 libboost-date-time1.74-dev i386 1.74.0-9 [250 kB] Get: 176 http://deb.debian.org/debian bullseye/main i386 libboost-dev i386 1.74.0.3 [4548 B] Get: 177 http://deb.debian.org/debian bullseye/main i386 libboost-regex1.74.0 i386 1.74.0-9 [542 kB] Get: 178 http://deb.debian.org/debian bullseye/main i386 libicu-dev i386 67.1-7 [9801 kB] Get: 179 http://deb.debian.org/debian bullseye/main i386 libboost-regex1.74-dev i386 1.74.0-9 [618 kB] Get: 180 http://deb.debian.org/debian bullseye/main i386 libboost-iostreams1.74-dev i386 1.74.0-9 [275 kB] Get: 181 http://deb.debian.org/debian bullseye/main i386 libboost-iostreams-dev i386 1.74.0.3 [4320 B] Get: 182 http://deb.debian.org/debian bullseye/main i386 libboost-python1.74.0 i386 1.74.0-9 [319 kB] Get: 183 http://deb.debian.org/debian bullseye/main i386 libpython3.9 i386 3.9.2-1 [1715 kB] Get: 184 http://deb.debian.org/debian bullseye/main i386 libexpat1-dev i386 2.2.10-2+deb11u5 [149 kB] Get: 185 http://deb.debian.org/debian bullseye/main i386 libpython3.9-dev i386 3.9.2-1 [3822 kB] Get: 186 http://deb.debian.org/debian bullseye/main i386 libpython3-dev i386 3.9.2-3 [21.7 kB] Get: 187 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2+deb11u2 [194 kB] Get: 188 http://deb.debian.org/debian bullseye/main i386 python3.9-dev i386 3.9.2-1 [515 kB] Get: 189 http://deb.debian.org/debian bullseye/main i386 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 190 http://deb.debian.org/debian bullseye/main i386 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 191 http://deb.debian.org/debian bullseye/main i386 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 192 http://deb.debian.org/debian bullseye/main i386 python3-dev i386 3.9.2-3 [24.8 kB] Get: 193 http://deb.debian.org/debian bullseye/main i386 libboost-python1.74-dev i386 1.74.0-9 [344 kB] Get: 194 http://deb.debian.org/debian bullseye/main i386 libboost-python-dev i386 1.74.0.3 [4632 B] Get: 195 http://deb.debian.org/debian bullseye/main i386 libboost-regex-dev i386 1.74.0.3 [4596 B] Get: 196 http://deb.debian.org/debian bullseye/main i386 libboost-system1.74.0 i386 1.74.0-9 [241 kB] Get: 197 http://deb.debian.org/debian bullseye/main i386 libboost-system1.74-dev i386 1.74.0-9 [243 kB] Get: 198 http://deb.debian.org/debian bullseye/main i386 libboost-system-dev i386 1.74.0.3 [4472 B] Get: 199 http://deb.debian.org/debian bullseye/main i386 libboost-thread1.74.0 i386 1.74.0-9 [282 kB] Get: 200 http://deb.debian.org/debian bullseye/main i386 libboost-thread1.74-dev i386 1.74.0-9 [294 kB] Get: 201 http://deb.debian.org/debian bullseye/main i386 libboost-thread-dev i386 1.74.0.3 [4356 B] Get: 202 http://deb.debian.org/debian bullseye/main i386 libbrotli-dev i386 1.0.9-2+b2 [287 kB] Get: 203 http://deb.debian.org/debian bullseye/main i386 libcairo-gobject2 i386 1.16.0-5 [125 kB] Get: 204 http://deb.debian.org/debian bullseye/main i386 libcmark-gfm0 i386 0.29.0.gfm.0-6 [122 kB] Get: 205 http://deb.debian.org/debian bullseye/main i386 libcmark-gfm-extensions0 i386 0.29.0.gfm.0-6 [47.8 kB] Get: 206 http://deb.debian.org/debian bullseye/main i386 libcommons-parent-java all 43-1 [10.8 kB] Get: 207 http://deb.debian.org/debian bullseye/main i386 libcommons-logging-java all 1.2-2 [62.2 kB] Get: 208 http://deb.debian.org/debian bullseye/main i386 libcoordgen1 i386 1.4.2-1 [212 kB] Get: 209 http://deb.debian.org/debian bullseye/main i386 libcoordgen-dev i386 1.4.2-1 [45.1 kB] Get: 210 http://deb.debian.org/debian bullseye/main i386 libdatrie1 i386 0.2.13-1 [44.5 kB] Get: 211 http://deb.debian.org/debian bullseye/main i386 pkg-config i386 0.29.2-1 [66.3 kB] Get: 212 http://deb.debian.org/debian bullseye/main i386 libeigen3-dev all 3.3.9-2 [858 kB] Get: 213 http://deb.debian.org/debian bullseye/main i386 libffi-dev i386 3.3-6 [54.7 kB] Get: 214 http://deb.debian.org/debian bullseye/main i386 libfontbox-java all 1:1.8.16-2 [211 kB] Get: 215 http://deb.debian.org/debian bullseye/main i386 libpng-dev i386 1.6.37-3 [307 kB] Get: 216 http://deb.debian.org/debian bullseye/main i386 libfreetype-dev i386 2.10.4+dfsg-1+deb11u1 [589 kB] Get: 217 http://deb.debian.org/debian bullseye/main i386 libfreetype6-dev i386 2.10.4+dfsg-1+deb11u1 [82.6 kB] Get: 218 http://deb.debian.org/debian bullseye/main i386 libfribidi0 i386 1.0.8-2+deb11u1 [65.6 kB] Get: 219 http://deb.debian.org/debian bullseye/main i386 libgdk-pixbuf2.0-common all 2.42.2+dfsg-1+deb11u1 [320 kB] Get: 220 http://deb.debian.org/debian bullseye/main i386 shared-mime-info i386 2.0-1 [703 kB] Get: 221 http://deb.debian.org/debian bullseye/main i386 libgdk-pixbuf-2.0-0 i386 2.42.2+dfsg-1+deb11u1 [156 kB] Get: 222 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 223 http://deb.debian.org/debian bullseye/main i386 libimagequant0 i386 2.12.2-1.1 [32.4 kB] Get: 224 http://deb.debian.org/debian bullseye/main i386 liblapack3 i386 3.9.0-3+deb11u1 [1960 kB] Get: 225 http://deb.debian.org/debian bullseye/main i386 libmaeparser1 i386 1.2.4-1+b1 [94.6 kB] Get: 226 http://deb.debian.org/debian bullseye/main i386 libmaeparser-dev i386 1.2.4-1+b1 [13.4 kB] Get: 227 http://deb.debian.org/debian bullseye/main i386 libncurses-dev i386 6.2+20201114-2+deb11u2 [373 kB] Get: 228 http://deb.debian.org/debian bullseye/main i386 libthai-data all 0.1.28-3 [170 kB] Get: 229 http://deb.debian.org/debian bullseye/main i386 libthai0 i386 0.1.28-3 [55.3 kB] Get: 230 http://deb.debian.org/debian bullseye/main i386 libpango-1.0-0 i386 1.46.2-3 [197 kB] Get: 231 http://deb.debian.org/debian bullseye/main i386 libpangoft2-1.0-0 i386 1.46.2-3 [65.1 kB] Get: 232 http://deb.debian.org/debian bullseye/main i386 libpangocairo-1.0-0 i386 1.46.2-3 [51.9 kB] Get: 233 http://deb.debian.org/debian bullseye/main i386 libpdfbox-java all 1:1.8.16-2 [5205 kB] Get: 234 http://deb.debian.org/debian bullseye/main i386 libpfm4 i386 4.11.1+git32-gd0b85fb-1 [235 kB] Get: 235 http://deb.debian.org/debian bullseye/main i386 libpq5 i386 13.11-0+deb11u1 [189 kB] Get: 236 http://deb.debian.org/debian bullseye/main i386 libpq-dev i386 13.11-0+deb11u1 [150 kB] Get: 237 http://deb.debian.org/debian bullseye/main i386 librsvg2-2 i386 2.50.3+dfsg-1+deb11u1 [2558 kB] Get: 238 http://deb.debian.org/debian bullseye/main i386 librsvg2-bin i386 2.50.3+dfsg-1+deb11u1 [36.4 kB] Get: 239 http://deb.debian.org/debian bullseye/main i386 libsqlite3-dev i386 3.34.1-3 [1001 kB] Get: 240 http://deb.debian.org/debian bullseye/main i386 libtinfo-dev i386 6.2+20201114-2+deb11u2 [936 B] Get: 241 http://deb.debian.org/debian bullseye/main i386 libyaml-0-2 i386 0.2.2-1 [51.7 kB] Get: 242 http://deb.debian.org/debian bullseye/main i386 libz3-dev i386 4.8.10-1 [90.8 kB] Get: 243 http://deb.debian.org/debian bullseye/main i386 llvm-11-runtime i386 1:11.0.1-2 [200 kB] Get: 244 http://deb.debian.org/debian bullseye/main i386 llvm-11 i386 1:11.0.1-2 [8580 kB] Get: 245 http://deb.debian.org/debian bullseye/main i386 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 246 http://deb.debian.org/debian bullseye/main i386 python3-pygments all 2.7.1+dfsg-2.1 [657 kB] Get: 247 http://deb.debian.org/debian bullseye/main i386 python3-yaml i386 5.3.1-5 [127 kB] Get: 248 http://deb.debian.org/debian bullseye/main i386 llvm-11-tools i386 1:11.0.1-2 [362 kB] Get: 249 http://deb.debian.org/debian bullseye/main i386 llvm-11-dev i386 1:11.0.1-2 [27.3 MB] Get: 250 http://deb.debian.org/debian bullseye/main i386 pandoc-data all 2.9.2.1-1+deb11u1 [377 kB] Get: 251 http://deb.debian.org/debian bullseye/main i386 pandoc i386 2.9.2.1-1+deb11u1 [19.1 MB] Get: 252 http://deb.debian.org/debian bullseye/main i386 postgresql-client-common all 225 [89.3 kB] Get: 253 http://deb.debian.org/debian bullseye/main i386 postgresql-client-13 i386 13.11-0+deb11u1 [1536 kB] Get: 254 http://deb.debian.org/debian bullseye/main i386 ssl-cert all 1.1.0+nmu1 [21.0 kB] Get: 255 http://deb.debian.org/debian bullseye/main i386 postgresql-common all 225 [237 kB] Get: 256 http://deb.debian.org/debian bullseye/main i386 postgresql-server-dev-13 i386 13.11-0+deb11u1 [1053 kB] Get: 257 http://deb.debian.org/debian bullseye/main i386 postgresql-server-dev-all all 225 [75.1 kB] Get: 258 http://deb.debian.org/debian bullseye/main i386 preview-latex-style all 12.2-1 [201 kB] Get: 259 http://deb.debian.org/debian bullseye/main i386 python-babel-localedata all 2.8.0+dfsg.1-7 [4997 kB] Get: 260 http://deb.debian.org/debian bullseye/main i386 python3-alabaster all 0.7.8-1.1 [18.6 kB] Get: 261 http://deb.debian.org/debian bullseye/main i386 python3-tz all 2021.1-1 [34.8 kB] Get: 262 http://deb.debian.org/debian bullseye/main i386 python3-babel all 2.8.0+dfsg.1-7 [100 kB] Get: 263 http://deb.debian.org/debian bullseye/main i386 python3-certifi all 2020.6.20-1 [151 kB] Get: 264 http://deb.debian.org/debian bullseye/main i386 python3-chardet all 4.0.0-1 [99.0 kB] Get: 265 http://deb.debian.org/debian bullseye/main i386 python3-commonmark all 0.9.1-3 [44.9 kB] Get: 266 http://deb.debian.org/debian bullseye/main i386 python3-six all 1.16.0-2 [17.5 kB] Get: 267 http://deb.debian.org/debian bullseye/main i386 python3-dateutil all 2.8.1-6 [79.2 kB] Get: 268 http://deb.debian.org/debian bullseye/main i386 python3-roman all 2.0.0-5 [9064 B] Get: 269 http://deb.debian.org/debian bullseye/main i386 python3-docutils all 0.16+dfsg-4 [384 kB] Get: 270 http://deb.debian.org/debian bullseye/main i386 python3-idna all 2.10-1 [37.4 kB] Get: 271 http://deb.debian.org/debian bullseye/main i386 python3-imagesize all 1.2.0-2 [5824 B] Get: 272 http://deb.debian.org/debian bullseye/main i386 python3-markupsafe i386 1.1.1-1+b3 [15.3 kB] Get: 273 http://deb.debian.org/debian bullseye/main i386 python3-jinja2 all 2.11.3-1 [114 kB] Get: 274 http://deb.debian.org/debian bullseye/main i386 python3-numpy i386 1:1.19.5-1 [3600 kB] Get: 275 http://deb.debian.org/debian bullseye/main i386 python3-pyparsing all 2.4.7-1 [109 kB] Get: 276 http://deb.debian.org/debian bullseye/main i386 python3-packaging all 20.9-2 [33.5 kB] Get: 277 http://deb.debian.org/debian bullseye/main i386 python3-pandas-lib i386 1.1.5+dfsg-2 [3182 kB] Get: 278 http://deb.debian.org/debian bullseye/main i386 python3-pandas all 1.1.5+dfsg-2 [2096 kB] Get: 279 http://deb.debian.org/debian bullseye/main i386 python3-pil i386 8.1.2+dfsg-0.3+deb11u1 [445 kB] Get: 280 http://deb.debian.org/debian bullseye/main i386 sphinx-common all 3.4.3-2 [578 kB] Get: 281 http://deb.debian.org/debian bullseye/main i386 python3-urllib3 all 1.26.5-1~exp1 [114 kB] Get: 282 http://deb.debian.org/debian bullseye/main i386 python3-requests all 2.25.1+dfsg-2 [69.3 kB] Get: 283 http://deb.debian.org/debian bullseye/main i386 python3-snowballstemmer all 2.1.0-1 [58.7 kB] Get: 284 http://deb.debian.org/debian bullseye/main i386 python3-sphinx all 3.4.3-2 [545 kB] Get: 285 http://deb.debian.org/debian bullseye/main i386 python3-recommonmark all 0.6.0+ds-1 [17.2 kB] Get: 286 http://deb.debian.org/debian bullseye/main i386 python3-sqlalchemy all 1.3.22+ds1-1 [795 kB] Get: 287 http://deb.debian.org/debian bullseye/main i386 rapidjson-dev all 1.1.0+dfsg2-7 [98.9 kB] Get: 288 http://deb.debian.org/debian bullseye/main i386 texlive-fonts-recommended all 2020.20210202-3 [5002 kB] Get: 289 http://deb.debian.org/debian bullseye/main i386 texlive-latex-recommended all 2020.20210202-3 [14.5 MB] Get: 290 http://deb.debian.org/debian bullseye/main i386 texlive-pictures all 2020.20210202-3 [6743 kB] Get: 291 http://deb.debian.org/debian bullseye/main i386 texlive-latex-extra all 2020.20210202-3 [13.7 MB] Fetched 317 MB in 5s (64.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17763 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8+deb11u1_i386.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../01-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../03-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_i386.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../05-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../06-m4_1.4.18-5_i386.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package flex. Preparing to unpack .../07-flex_2.6.4-8_i386.deb ... Unpacking flex (2.6.4-8) ... Selecting previously unselected package libfftw3-double3:i386. Preparing to unpack .../08-libfftw3-double3_3.3.8-2_i386.deb ... Unpacking libfftw3-double3:i386 (3.3.8-2) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../09-libexpat1_2.2.10-2+deb11u5_i386.deb ... Unpacking libexpat1:i386 (2.2.10-2+deb11u5) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../10-libbrotli1_1.0.9-2+b2_i386.deb ... Unpacking libbrotli1:i386 (1.0.9-2+b2) ... Selecting previously unselected package libpng16-16:i386. Preparing to unpack .../11-libpng16-16_1.6.37-3_i386.deb ... Unpacking libpng16-16:i386 (1.6.37-3) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../12-libfreetype6_2.10.4+dfsg-1+deb11u1_i386.deb ... Unpacking libfreetype6:i386 (2.10.4+dfsg-1+deb11u1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../13-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package ucf. Preparing to unpack .../14-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../15-fonts-dejavu-core_2.37-2_all.deb ... Unpacking fonts-dejavu-core (2.37-2) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../16-fontconfig-config_2.13.1-4.2_all.deb ... Unpacking fontconfig-config (2.13.1-4.2) ... Selecting previously unselected package libfontconfig1:i386. Preparing to unpack .../17-libfontconfig1_2.13.1-4.2_i386.deb ... Unpacking libfontconfig1:i386 (2.13.1-4.2) ... Selecting previously unselected package libaom0:i386. Preparing to unpack .../18-libaom0_1.0.0.errata1-3+deb11u1_i386.deb ... Unpacking libaom0:i386 (1.0.0.errata1-3+deb11u1) ... Selecting previously unselected package libdav1d4:i386. Preparing to unpack .../19-libdav1d4_0.7.1-3_i386.deb ... Unpacking libdav1d4:i386 (0.7.1-3) ... Selecting previously unselected package libde265-0:i386. Preparing to unpack .../20-libde265-0_1.0.11-0+deb11u1_i386.deb ... Unpacking libde265-0:i386 (1.0.11-0+deb11u1) ... Selecting previously unselected package libnuma1:i386. Preparing to unpack .../21-libnuma1_2.0.12-1+b1_i386.deb ... Unpacking libnuma1:i386 (2.0.12-1+b1) ... Selecting previously unselected package libx265-192:i386. Preparing to unpack .../22-libx265-192_3.4-2_i386.deb ... Unpacking libx265-192:i386 (3.4-2) ... Selecting previously unselected package libheif1:i386. Preparing to unpack .../23-libheif1_1.11.0-1_i386.deb ... Unpacking libheif1:i386 (1.11.0-1) ... Selecting previously unselected package libjbig0:i386. Preparing to unpack .../24-libjbig0_2.1-3.1+b2_i386.deb ... Unpacking libjbig0:i386 (2.1-3.1+b2) ... Selecting previously unselected package libjpeg62-turbo:i386. Preparing to unpack .../25-libjpeg62-turbo_1%3a2.0.6-4_i386.deb ... Unpacking libjpeg62-turbo:i386 (1:2.0.6-4) ... Selecting previously unselected package liblcms2-2:i386. Preparing to unpack .../26-liblcms2-2_2.12~rc1-2_i386.deb ... Unpacking liblcms2-2:i386 (2.12~rc1-2) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../27-libglib2.0-0_2.66.8-1_i386.deb ... Unpacking libglib2.0-0:i386 (2.66.8-1) ... Selecting previously unselected package liblqr-1-0:i386. Preparing to unpack .../28-liblqr-1-0_0.4.2-2.1_i386.deb ... Unpacking liblqr-1-0:i386 (0.4.2-2.1) ... Selecting previously unselected package libltdl7:i386. Preparing to unpack .../29-libltdl7_2.4.6-15_i386.deb ... Unpacking libltdl7:i386 (2.4.6-15) ... Selecting previously unselected package libopenjp2-7:i386. Preparing to unpack .../30-libopenjp2-7_2.4.0-3_i386.deb ... Unpacking libopenjp2-7:i386 (2.4.0-3) ... Selecting previously unselected package libdeflate0:i386. Preparing to unpack .../31-libdeflate0_1.7-1_i386.deb ... Unpacking libdeflate0:i386 (1.7-1) ... Selecting previously unselected package libwebp6:i386. Preparing to unpack .../32-libwebp6_0.6.1-2.1+deb11u2_i386.deb ... Unpacking libwebp6:i386 (0.6.1-2.1+deb11u2) ... Selecting previously unselected package libtiff5:i386. Preparing to unpack .../33-libtiff5_4.2.0-1+deb11u4_i386.deb ... Unpacking libtiff5:i386 (4.2.0-1+deb11u4) ... Selecting previously unselected package libwebpdemux2:i386. Preparing to unpack .../34-libwebpdemux2_0.6.1-2.1+deb11u2_i386.deb ... Unpacking libwebpdemux2:i386 (0.6.1-2.1+deb11u2) ... Selecting previously unselected package libwebpmux3:i386. Preparing to unpack .../35-libwebpmux3_0.6.1-2.1+deb11u2_i386.deb ... Unpacking libwebpmux3:i386 (0.6.1-2.1+deb11u2) ... Selecting previously unselected package libxau6:i386. Preparing to unpack .../36-libxau6_1%3a1.0.9-1_i386.deb ... Unpacking libxau6:i386 (1:1.0.9-1) ... Selecting previously unselected package libmd0:i386. Preparing to unpack .../37-libmd0_1.0.3-3_i386.deb ... Unpacking libmd0:i386 (1.0.3-3) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../38-libbsd0_0.11.3-1+deb11u1_i386.deb ... 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Adding 'diversion of /usr/bin/pg_config to /usr/bin/pg_config.libpq-dev by postgresql-common' Unpacking postgresql-common (225) ... Selecting previously unselected package postgresql-server-dev-13. Preparing to unpack .../193-postgresql-server-dev-13_13.11-0+deb11u1_i386.deb ... Unpacking postgresql-server-dev-13 (13.11-0+deb11u1) ... Selecting previously unselected package postgresql-server-dev-all. Preparing to unpack .../194-postgresql-server-dev-all_225_all.deb ... Unpacking postgresql-server-dev-all (225) ... Selecting previously unselected package preview-latex-style. Preparing to unpack .../195-preview-latex-style_12.2-1_all.deb ... Unpacking preview-latex-style (12.2-1) ... Selecting previously unselected package python-babel-localedata. Preparing to unpack .../196-python-babel-localedata_2.8.0+dfsg.1-7_all.deb ... Unpacking python-babel-localedata (2.8.0+dfsg.1-7) ... Selecting previously unselected package python3-alabaster. 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Setting up imagemagick-6-common (8:6.9.11.60+dfsg-1.3+deb11u1) ... Setting up libpsl5:i386 (0.21.0-1.2) ... Setting up libboost1.74-dev:i386 (1.74.0-9) ... Setting up libboost-atomic1.74.0:i386 (1.74.0-9) ... Setting up bsdextrautils (2.36.1-8+deb11u1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up hicolor-icon-theme (0.17-2) ... Setting up libicu67:i386 (67.1-7) ... Setting up libdatrie1:i386 (0.2.13-1) ... Setting up libmagic-mgc (1:5.39-3+deb11u1) ... Setting up libtexlua53:i386 (2020.20200327.54578-7+deb11u1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:i386 (0.2.2-1) ... Setting up libglib2.0-0:i386 (2.66.8-1) ... No schema files found: doing nothing. Setting up libaom0:i386 (1.0.0.errata1-3+deb11u1) ... Setting up libtexluajit2:i386 (2020.20200327.54578-7+deb11u1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:i386 (1.0.9-2+b2) ... Setting up libfontbox-java (1:1.8.16-2) ... Setting up libboost-chrono1.74-dev:i386 (1.74.0-9) ... Setting up libgdk-pixbuf2.0-common (2.42.2+dfsg-1+deb11u1) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:i386 (1.43.0-1) ... Setting up libmagic1:i386 (1:5.39-3+deb11u1) ... Setting up libdeflate0:i386 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up libzzip-0-13:i386 (0.13.62-3.3+deb11u1) ... Setting up file (1:5.39-3+deb11u1) ... Setting up libffi-dev:i386 (3.3-6) ... Setting up libjbig0:i386 (2.1-3.1+b2) ... Setting up python-babel-localedata (2.8.0+dfsg.1-7) ... Setting up rapidjson-dev (1.1.0+dfsg2-7) ... Setting up libmaeparser1:i386 (1.2.4-1+b1) ... Setting up libsasl2-modules-db:i386 (2.1.27+dfsg-2.1+deb11u1) ... Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Feb 11 00:22:03 UTC 2025. Universal Time is now: Tue Feb 11 00:22:03 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20180224.1+nmu1) ... Setting up libz3-4:i386 (4.8.10-1) ... Setting up libblas3:i386 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libuv1:i386 (1.40.0-2) ... Setting up libpfm4:i386 (4.11.1+git32-gd0b85fb-1) ... Setting up libexpat1-dev:i386 (2.2.10-2+deb11u5) ... Setting up libjpeg62-turbo:i386 (1:2.0.6-4) ... Setting up libsqlite3-dev:i386 (3.34.1-3) ... Setting up libx11-data (2:1.7.2-1+deb11u1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libteckit0:i386 (2.5.10+ds1-3) ... Setting up libapache-pom-java (18-1) ... Setting up libboost-system1.74-dev:i386 (1.74.0-9) ... Setting up libncurses6:i386 (6.2+20201114-2+deb11u2) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up libfribidi0:i386 (1.0.8-2+deb11u1) ... Setting up libboost-regex1.74.0:i386 (1.74.0-9) ... Setting up t1utils (1.41-4) ... Setting up libimagequant0:i386 (2.12.2-1.1) ... Setting up libpng16-16:i386 (1.6.37-3) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:i386 (0.6.1-2.1+deb11u2) ... Setting up icu-devtools (67.1-7) ... Setting up pkg-config (0.29.2-1) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libcmark-gfm0:i386 (0.29.0.gfm.0-6) ... Setting up libgc1:i386 (1:8.0.4-3) ... Setting up libltdl7:i386 (2.4.6-15) ... Setting up libfftw3-double3:i386 (3.3.8-2) ... Setting up libkpathsea6:i386 (2020.20200327.54578-7+deb11u1) ... Setting up libsasl2-2:i386 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libgfortran5:i386 (10.2.1-6) ... Setting up libjsoncpp24:i386 (1.9.4-4) ... Setting up libboost-atomic1.74-dev:i386 (1.74.0-9) ... Setting up libboost-serialization1.74.0:i386 (1.74.0-9) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2+deb11u2) ... Setting up libnuma1:i386 (2.0.12-1+b1) ... Setting up libmd0:i386 (1.0.3-3) ... Setting up libcoordgen1:i386 (1.4.2-1) ... Setting up liblqr-1-0:i386 (0.4.2-2.1) ... Setting up sensible-utils (0.0.14) ... Setting up librhash0:i386 (1.4.1-2) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libmpdec3:i386 (2.5.1-1) ... Setting up fonts-lmodern (2.004.5-6.1) ... Setting up libdav1d4:i386 (0.7.1-3) ... Setting up libopenjp2-7:i386 (2.4.0-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libthai-data (0.1.28-3) ... Setting up libssh2-1:i386 (1.9.0-2) ... Setting up netbase (6.3) ... Setting up sgml-base (1.30) ... Setting up cmake-data (3.18.4-2+deb11u1) ... Setting up libboost-dev:i386 (1.74.0.3) ... Setting up libtiff5:i386 (4.2.0-1+deb11u4) ... Setting up pandoc-data (2.9.2.1-1+deb11u1) ... Setting up libcoordgen-dev:i386 (1.4.2-1) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up libboost-date-time1.74.0:i386 (1.74.0-9) ... Setting up libc6-amd64 (2.31-13+deb11u6) ... Setting up libboost-python1.74.0 (1.74.0-9) ... Setting up libde265-0:i386 (1.0.11-0+deb11u1) ... Setting up openssl (1.1.1w-0+deb11u1) ... Setting up libwebpmux3:i386 (0.6.1-2.1+deb11u2) ... Setting up libbsd0:i386 (0.11.3-1+deb11u1) ... Setting up mailcap (3.69) ... Setting up libelf1:i386 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libicu-dev:i386 (67.1-7) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7+deb11u4) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libbrotli-dev:i386 (1.0.9-2+b2) ... Setting up libprocps8:i386 (2:3.3.17-5) ... Setting up libsynctex2:i386 (2020.20200327.54578-7+deb11u1) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libboost-thread1.74.0:i386 (1.74.0-9) ... Setting up libmaeparser-dev:i386 (1.2.4-1+b1) ... Setting up postgresql-client-common (225) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libz3-dev:i386 (4.8.10-1) ... Setting up libice6:i386 (2:1.0.10-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up liblapack3:i386 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up libncurses-dev:i386 (6.2+20201114-2+deb11u2) ... Setting up libxcb1:i386 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libpdfbox-java (1:1.8.16-2) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:i386 (3.4.3-2+deb11u1) ... Setting up libxcb-render0:i386 (1.14-3) ... Setting up libwebpdemux2:i386 (0.6.1-2.1+deb11u2) ... Setting up libedit2:i386 (3.1-20191231-2+b1) ... Setting up libreadline8:i386 (8.1-1) ... Setting up libboost-system-dev:i386 (1.74.0.3) ... Setting up libpng-dev:i386 (1.6.37-3) ... Setting up libcommons-parent-java (43-1) ... Setting up libx265-192:i386 (3.4-2) ... Setting up lib64atomic1 (10.2.1-6) ... Setting up libcommons-logging-java (1.2-2) ... Setting up libldap-2.4-2:i386 (2.4.57+dfsg-3+deb11u1) ... Setting up m4 (1.4.18-5) ... Setting up libobjc4:i386 (10.2.1-6) ... Setting up libxcb-shm0:i386 (1.14-3) ... Setting up libcmark-gfm-extensions0:i386 (0.29.0.gfm.0-6) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libthai0:i386 (0.1.28-3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up lib64gcc-s1 (10.2.1-6) ... Setting up libllvm11:i386 (1:11.0.1-2) ... Setting up libptexenc1:i386 (2020.20200327.54578-7+deb11u1) ... Setting up pandoc (2.9.2.1-1+deb11u1) ... Setting up libfreetype6:i386 (2.10.4+dfsg-1+deb11u1) ... Setting up ssl-cert (1.1.0+nmu1) ... Setting up shared-mime-info (2.0-1) ... Setting up libeigen3-dev (3.3.9-2) ... Setting up libclang1-11 (1:11.0.1-2) ... Setting up ucf (3.0043) ... Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up autoconf (2.69-14) ... Setting up libboost-serialization1.74-dev:i386 (1.74.0-9) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up libobjc-10-dev:i386 (10.2.1-6) ... Setting up dwz (0.13+20210201-1) ... Setting up libboost-regex1.74-dev:i386 (1.74.0-9) ... Setting up groff-base (1.22.4-6) ... Setting up xml-core (0.18+nmu1) ... Setting up procps (2:3.3.17-5) ... Setting up bison (2:3.7.5+dfsg-1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up libcurl4:i386 (7.74.0-1.3+deb11u9) ... Setting up libx11-6:i386 (2:1.7.2-1+deb11u1) ... Setting up libharfbuzz0b:i386 (2.7.4-1) ... Setting up libgdk-pixbuf-2.0-0:i386 (2.42.2+dfsg-1+deb11u1) ... Setting up libboost-regex-dev:i386 (1.74.0.3) ... Setting up libsm6:i386 (2:1.2.3-1) ... Setting up libpython3.9-stdlib:i386 (3.9.2-1) ... Setting up libpython3-stdlib:i386 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libtinfo-dev:i386 (6.2+20201114-2+deb11u2) ... Setting up libpaper1:i386 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up flex (2.6.4-8) ... Setting up llvm-11-runtime (1:11.0.1-2) ... Setting up libxpm4:i386 (1:3.5.12-1.1~deb11u1) ... Setting up libxrender1:i386 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libheif1:i386 (1.11.0-1) ... Setting up libpq5:i386 (13.11-0+deb11u1) ... Setting up libxext6:i386 (2:1.3.3-1.1) ... Setting up llvm-11 (1:11.0.1-2) ... Setting up libpq-dev (13.11-0+deb11u1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libfreetype-dev:i386 (2.10.4+dfsg-1+deb11u1) ... Setting up postgresql-client-13 (13.11-0+deb11u1) ... update-alternatives: using /usr/share/postgresql/13/man/man1/psql.1.gz to provide /usr/share/man/man1/psql.1.gz (psql.1.gz) in auto mode Setting up libclang-cpp11 (1:11.0.1-2) ... Setting up libboost-iostreams1.74-dev:i386 (1.74.0-9) ... Setting up lib64stdc++6 (10.2.1-6) ... Setting up dh-autoreconf (20) ... Setting up tex-common (6.16) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libboost-date-time1.74-dev:i386 (1.74.0-9) ... Setting up doxygen (1.9.1-1) ... Setting up libpython3.9:i386 (3.9.2-1) ... Setting up sphinx-common (3.4.3-2) ... Setting up postgresql-common (225) ... ERROR: ld.so: object 'libeatmydata.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. Adding user postgres to group ssl-cert 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 libxt6:i386 (1:1.2.0-1) ... Setting up libclang-common-11-dev (1:11.0.1-2) ... Setting up cmake (3.18.4-2+deb11u1) ... Setting up libboost-thread1.74-dev:i386 (1.74.0-9) ... Setting up libfontconfig1:i386 (2.13.1-4.2) ... Setting up clang-11 (1:11.0.1-2) ... Setting up python3.9 (3.9.2-1) ... Setting up libboost-thread-dev:i386 (1.74.0.3) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxmu6:i386 (2:1.1.2-2+b3) ... Setting up libxi6:i386 (2:1.7.10-1) ... Setting up preview-latex-style (12.2-1) ... Setting up libpango-1.0-0:i386 (1.46.2-3) ... Setting up libpython3.9-dev:i386 (3.9.2-1) ... 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Setting up texlive-binaries (2020.20200327.54578-7+deb11u1) ... 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 libmagickwand-6.q16-6:i386 (8:6.9.11.60+dfsg-1.3+deb11u1) ... Setting up python3-dateutil (2.8.1-6) ... Setting up libcairo-gobject2:i386 (1.16.0-5) ... Setting up libpangoft2-1.0-0:i386 (1.46.2-3) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up texlive-base (2020.20210202-3) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libpangocairo-1.0-0:i386 (1.46.2-3) ... 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Setting up imagemagick-6.q16 (8:6.9.11.60+dfsg-1.3+deb11u1) ... 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-fonts-recommended (2020.20210202-3) ... 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Setting up python3-docutils (0.16+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3-sphinx (3.4.3-2) ... Setting up python3-recommonmark (0.6.0+ds-1) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.16) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/110048/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bullseye I: user script /srv/workspace/pbuilder/110048/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/rdkit-202009.4/ && 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_202009.4-1_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202009.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael Banck dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean pg_buildext checkcontrol dh clean --with python3 --buildsystem=cmake --parallel dh: warning: Compatibility levels before 10 are deprecated (level 9 in use) debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/rdkit-202009.4' find /build/reproducible-path/rdkit-202009.4 -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 dh_auto_clean: warning: Compatibility levels before 10 are deprecated (level 9 in use) pg_buildext clean /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit build-%v rm -rf build-*/ make[1]: Leaving directory '/build/reproducible-path/rdkit-202009.4' dh_clean -O--buildsystem=cmake -O--parallel dh_clean: warning: Compatibility levels before 10 are deprecated (level 9 in use) debian/rules build dh build --with python3 --buildsystem=cmake --parallel dh: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_update_autotools_config -O--buildsystem=cmake -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/rdkit-202009.4' 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 -DRDK_BUILD_PYTHON_WRAPPERS=ON -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_USE_URF=OFF -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DPYTHON_EXECUTABLE=/usr/bin/python3.9 ../ dh_auto_configure: warning: Compatibility levels before 10 are deprecated (level 9 in use) cd obj-i686-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=ON -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_THREADSAFE_SSS=ON -DRDK_BUILD_PYTHON_WRAPPERS=ON -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_USE_URF=OFF -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DPYTHON_EXECUTABLE=/usr/bin/python3.9 ../ .. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- 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 -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Found Catch2: /usr/include/catch2 CATCH: /usr/include/catch2 -- Found PythonInterp: /usr/bin/python3.9 (found version "3.9.2") -- Found PythonLibs: /usr/lib/i386-linux-gnu/libpython3.9.so (found version "3.9.2") CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:279 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:279 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:2018 (message): No header defined for python-py39; skipping header check (note: header-only libraries have no designated component) Call Stack (most recent call first): CMakeLists.txt:279 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:279 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:279 (find_package) Python Install directory /usr/lib/python3/dist-packages PYTHON Py_ENABLE_SHARED: 1 PYTHON USING LINK LINE: -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:387 (find_package) -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.58.0") found components: serialization == Using strict rotor definition CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) External/CoordGen/CMakeLists.txt:9 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) External/CoordGen/CMakeLists.txt:9 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) External/CoordGen/CMakeLists.txt:9 (find_package) -- 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 CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) Code/RDStreams/CMakeLists.txt:4 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) Code/RDStreams/CMakeLists.txt:4 (find_package) -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.58.0") found components: iostreams regex CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) Code/GraphMol/FileParsers/CMakeLists.txt:21 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) Code/GraphMol/FileParsers/CMakeLists.txt:21 (find_package) CMake Warning at /usr/share/cmake-3.18/Modules/FindBoost.cmake:1187 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/share/cmake-3.18/Modules/FindBoost.cmake:1311 (_Boost_COMPONENT_DEPENDENCIES) /usr/share/cmake-3.18/Modules/FindBoost.cmake:1919 (_Boost_MISSING_DEPENDENCIES) Code/GraphMol/FileParsers/CMakeLists.txt:21 (find_package) -- 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 "1.2.11") == Updating Filters.cpp from pains file == Done updating pains files -- Found Freetype: /usr/lib/i386-linux-gnu/libfreetype.so (found version "2.10.4") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu make[1]: Leaving directory '/build/reproducible-path/rdkit-202009.4' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202009.4' dh_auto_build dh_auto_build: warning: Compatibility levels before 10 are deprecated (level 9 in use) cd obj-i686-linux-gnu && make -j15 VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202009.4 -B/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/depend make -f 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'/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/INCHI-API /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/CoordGen 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"/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/catch/CMakeFiles/catch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/catch/CMakeFiles/catch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/catch/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/catch/CMakeFiles/catch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/RingFamilies/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/CoordGen/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/depend.internal". 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Scanning dependencies of target RDStreams Scanning dependencies of target hc make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/build make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Scanning dependencies of target RDGeneral make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 0%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -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 -o CMakeFiles/hc.dir/hcdriver.c.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/Cluster/Murtagh/hcdriver.c [ 0%] Building CXX object Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o [ 0%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -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 -o CMakeFiles/hc.dir/hc.c.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/Cluster/Murtagh/hc.c [ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o [ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDStreams && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RDSTREAMS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDStreams_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDStreams.dir/streams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDStreams/streams.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/types.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/types.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/utils.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDLog.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/Invariant.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/versions.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/LocaleSwitcher.cpp [ 1%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2020.09.4 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o -lpthread cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2020.09.4 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 1%] Built target hc [ 1%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2020.09.4 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/i386-linux-gnu/libboost_iostreams.so -lpthread /usr/lib/i386-linux-gnu/libboost_regex.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2020.09.4 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 1%] Built target RDStreams [ 1%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2020.09.4 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -ldl -lpthread cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeneral.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1 ../../lib/libRDKitRDGeneral.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 1%] Built target RDGeneral make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --color= make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/RDBoost /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDBoost /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake --color= make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/RDGeneral /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/RDGeneral /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/RDGeneral /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake --color= make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Catalogs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Catalogs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --color= make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Query /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Query /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/depend.internal". Scanning dependencies of target testConcurrentQueue Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDBoost/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/depend.internal". make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Scanning dependencies of target testMatrices Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/depend.internal". Scanning dependencies of target EigenSolvers Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/depend.internal". make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Scanning dependencies of target RDBoost Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Catalogs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/depend.internal". make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Query/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/depend.internal". Scanning dependencies of target testDict Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend.internal". Scanning dependencies of target testRDValue Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend.internal". make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build Scanning dependencies of target testMatCalc make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build Scanning dependencies of target testQuery Scanning dependencies of target Catalogs make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Scanning dependencies of target SimDivPickers make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/testConcurrentQueue.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 1%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o [ 1%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMatrices.dir/testMatrices.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/testMatrices.cpp Scanning dependencies of target DataStructs make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o [ 1%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/testRDValue.cpp cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testDict.dir/testDict.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/testDict.cpp [ 1%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.cpp cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp [ 1%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o [ 1%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o [ 1%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o [ 1%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o [ 1%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Query && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testQuery.dir/test.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Query/test.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Catalogs/Catalog.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Catalogs/CatalogParams.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -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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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/MaxMinPicker.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/usr/include/catch2 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-I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/DiscreteValueVect.cpp [ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/FPBReader.cpp [ 5%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2020.09.4 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 5%] Built target SimDivPickers [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/MultiFPBReader.cpp [ 5%] Linking CXX shared library ../../lib/libRDKitCatalogs.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2020.09.4 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 5%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 5%] Built target Catalogs make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend.internal". Scanning dependencies of target testSimDivPickers make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/testPickers.cpp cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 5%] Built target EigenSolvers 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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 5%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/RDBoost.dir/Wrap.cpp.o ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 5%] Built target RDBoost make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= [ 5%] Linking CXX executable testMatrices cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend.internal". Scanning dependencies of target rdBase make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 -lpthread -ldl Scanning dependencies of target Clustering make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build [ 5%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDBoost/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdBase_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap/RDBase.cpp [ 5%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/Cluster/Murtagh/Clustering.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 5%] Built target testMatrices [ 5%] Linking CXX executable testSimDivPickers cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../lib/libRDKithc.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 5%] Built target testSimDivPickers [ 5%] Linking CXX executable testQuery cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 5%] Built target testQuery [ 5%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 5%] Built target DataStructs make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend 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-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend.internal". Scanning dependencies of target testFPB make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Scanning dependencies of target testMultiFPB make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build Scanning dependencies of target testDataStructs Scanning dependencies of target rdMetricMatrixCalc make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Scanning dependencies of target InfoTheory make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Scanning dependencies of target RDGeometryLib make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build Scanning dependencies of target pickersTestsCatch make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' Scanning dependencies of target cDataStructs make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build [ 5%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o [ 5%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/testDatastructs.cpp [ 5%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o [ 5%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o [ 5%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/testFPB.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/InfoBitRanker.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/testMultiFPB.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp [ 5%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o [ 5%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o [ 5%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.cpp Scanning dependencies of target rdSimDivPickers [ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -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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-I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/Transform3D.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/catch_tests.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 6%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/DataStructs.cpp [ 6%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/MaxMinPicker.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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 7%] Linking CXX executable testRDValue cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 7%] Built target testRDValue [ 7%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/DiscreteValueVect.cpp In file included from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap/RDBase.cpp:14: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ [ 7%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so -lpthread make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 7%] Built target Clustering [ 7%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/SparseIntVect.cpp [ 7%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/UniformGrid3D.cpp [ 8%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/GridUtils.cpp [ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_SparseBV.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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/libRDKitInfoTheory.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2020.09.4 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' 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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ [ 8%] Built target InfoTheory 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend.internal". Scanning dependencies of target rdInfoTheory make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 8%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap/InfoBitRanker.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 8%] Linking CXX executable testDict cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 8%] Built target testDict 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ML/Data /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/Data /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/depend.internal". 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Scanning dependencies of target cQuantize make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 8%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcQuantize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/Data/cQuantize.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/DiscreteValueVect.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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 /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:15: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ [ 8%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp [ 8%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 8%] Linking CXX executable testFPB cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 8%] Linking CXX executable testMultiFPB cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 8%] Built target RDGeometryLib make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= [ 8%] Built target testFPB 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend.internal". Scanning dependencies of target Alignment make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 8%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/AlignPoints.cpp [ 8%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 8%] Built target testMultiFPB make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake --color= Scanning dependencies of target GraphMol make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend.internal". [ 8%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Atom.cpp Scanning dependencies of target geometryTestsCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 8%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/catch_tests.cpp [ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 8%] Built target rdMetricMatrixCalc make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/depend.internal". Scanning dependencies of target testGrid make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 8%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/testGrid.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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:19: /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/PickerHelpers.h: In function 'RDKit::INT_VECT RDPickers::MaxMinPicker::lazyPick(T&, unsigned int, unsigned int, const INT_VECT&, int, double&) const [with T = pyobjFunctor]': /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/PickerHelpers.h:53:48: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 53 | return python::extract(dp_obj(i, j)); | ^ /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/PickerHelpers.h:53:48: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 53 | return python::extract(dp_obj(i, j)); | ^ [ 8%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/LeaderPicker.cpp [ 8%] Linking CXX shared library ../../../lib/libRDKitAlignment.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 8%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so -lpthread cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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-202009.4/obj-i686-linux-gnu' [ 8%] Built target Alignment make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/depend.internal". Scanning dependencies of target testTransforms make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 8%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/testTransforms.cpp [ 8%] Built target cQuantize 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend.internal". Scanning dependencies of target rdGeometry make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 8%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap/Point.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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_ExplicitBV.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_FPB.cpp [ 8%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202009.4/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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_BitOps.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 8%] Linking CXX executable testGrid cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 8%] Built target testGrid make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/depend.internal". Scanning dependencies of target testConrec make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 8%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/testConrec.cpp 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend.internal". Scanning dependencies of target testAlignment make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 8%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/testAlignment.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:186:56: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:156:58: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:404:16: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 404 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_Utils.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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 8%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryAtom.cpp [ 8%] Linking CXX executable testTransforms cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 8%] Built target testTransforms 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend.internal". Scanning dependencies of target rdAlignment make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 8%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAlignment_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/Wrap/rdAlignment.cpp [ 9%] Linking CXX executable testDataStructs cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 9%] Built target testDataStructs make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend.internal". Scanning dependencies of target ChemicalFeatures make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 9%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/FreeChemicalFeature.cpp In file included from /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/LeaderPicker.cpp:19: /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/PickerHelpers.h: In member function 'unsigned int RDPickers::LeaderPickerState::compact(int*, int*, unsigned int) [with T = pyobjFunctor]': /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/PickerHelpers.h:53:48: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 53 | return python::extract(dp_obj(i, j)); | ^ [ 9%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 9%] Linking CXX executable testAlignment cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 9%] Built target rdInfoTheory [ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryBond.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 9%] Built target testAlignment [ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Bond.cpp [ 9%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp [ 9%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2020.09.4 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 9%] 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend.internal". Scanning dependencies of target testChemicalFeatures make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 9%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/testChemicalFeatures.cpp In file included from /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/SparseIntVect.cpp:18: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = long long int]': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ 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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = long long unsigned int]': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ [ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolOps.cpp [ 9%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap/UniformGrid3D.cpp [ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202009.4/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/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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:16: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ [ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ROMol.cpp [ 9%] Linking CXX executable testChemicalFeatures cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 9%] Built target testChemicalFeatures [ 10%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RWMol.cpp [ 10%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 10%] Built target rdAlignment [ 10%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PeriodicTable.cpp [ 11%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp [ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/atomic_data.cpp /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FindRings.cpp:1367:36: warning: unused parameter 'mol' [-Wunused-parameter] 1367 | void findRingFamilies(const ROMol &mol) { | ~~~~~~~~~~~~~^~~ [ 12%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap/rdGeometry.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryOps.cpp [ 13%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 13%] Built target cDataStructs [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.cpp [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Canon.cpp [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/AtomIterators.cpp [ 13%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKithc.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 13%] Built target rdSimDivPickers [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/BondIterators.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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Aromaticity.cpp /build/reproducible-path/rdkit-202009.4/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-202009.4/Code/GraphMol/MolPickler.cpp:1139:39: required from 'static void RDKit::MolPickler::_depickle(std::istream&, RDKit::ROMol*, int, int) [with T = int; std::istream = std::basic_istream]' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.cpp:928:59: required from here /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.cpp:1684:37: warning: comparison is always false due to limited range of data type [-Wtype-limits] 1684 | if ((tmpChar < 0 || tmpChar > 127) && version > 9000) { | ~~~~~~~~^~~~~ /build/reproducible-path/rdkit-202009.4/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-202009.4/Code/GraphMol/MolPickler.cpp:1139:39: required from 'static void RDKit::MolPickler::_depickle(std::istream&, RDKit::ROMol*, int, int) [with T = unsigned char; std::istream = std::basic_istream]' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.cpp:930:65: required from here /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.cpp:1684:37: warning: comparison is always false due to limited range of data type [-Wtype-limits] [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Kekulize.cpp [ 14%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDiscriminators.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 14%] Built target rdGeometry [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ConjugHybrid.cpp [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/AddHs.cpp [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 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'/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 14%] Built target rdBase [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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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++11 -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Renumber.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/AdjustQuery.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 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-DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StereoGroup.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/new_canon.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstanceGroup.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/FindStereo.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FindStereo.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-202009.4/Code/GraphMol/ROMol.h:27, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/GraphMol.h:19, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ [ 15%] Linking CXX executable pickersTestsCatch cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../../lib/libRDKitSimDivPickers.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKithc.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 15%] Built target pickersTestsCatch [ 16%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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/MolDiscriminators.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 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1 ../../lib/libRDKitGraphMol.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 16%] Built target GraphMol make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake --color= make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake --color= 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --color= make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend.internal". Scanning dependencies of target Trajectory make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Scanning dependencies of target PartialCharges make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' Scanning dependencies of target MolCatalog Scanning dependencies of target SubstructMatch Scanning dependencies of target MolInterchange Scanning dependencies of target rdChemicalFeatures Scanning dependencies of target rdqueries Scanning dependencies of target Subgraphs make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build 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-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Scanning dependencies of target SLNParse make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build [ 16%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/GasteigerCharges.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/GasteigerParams.cpp [ 17%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o [ 17%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/rapidjson -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/Parser.cpp [ 17%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o Scanning dependencies of target SmilesParse cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp [ 17%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct/SubstructMatch.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs/Subgraphs.cpp make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build [ 17%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rdqueries.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 18%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/SLNParse.cpp [ 18%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesParse.cpp Scanning dependencies of target CIPLabeler make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make 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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++11 -o CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPMol.cpp Scanning dependencies of target MolTransforms make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 18%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms/MolTransforms.cpp [ 18%] Linking CXX executable geometryTestsCatch cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 18%] Built target geometryTestsCatch [ 18%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/Wrap/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/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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct/SubstructUtils.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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPLabeler.cpp [ 19%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Mancude.cpp [ 19%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 19%] Built target PartialCharges 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend.internal". Scanning dependencies of target rdPartialCharges make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 19%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdPartialCharges_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp [ 20%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalogParams.cpp [ 20%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script 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Scanning dependencies of target Optimizer make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 20%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer/BFGSOpt.cpp [ 20%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Queries.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 20%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs/SubgraphUtils.cpp [ 20%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 21%] Linking CXX executable testConrec cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2020.09.4 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 21%] 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend.internal". 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp [ 21%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer/LinearSearch.cpp [ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesParseOps.cpp [ 21%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 21%] Built target MolTransforms make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap 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Scanning dependencies of target rdMolTransforms make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 21%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Digraph.cpp [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Node.cpp [ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesWrite.cpp [ 21%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 21%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 21%] Built target rdChemicalFeatures 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend.internal". [ 21%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/rapidjson -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/Writer.cpp Scanning dependencies of target ShapeHelpers make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 21%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o [ 21%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 21%] Built target SubstructMatch make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend.internal". cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so Scanning dependencies of target MolAlign make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 21%] Built target Optimizer make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend [ 21%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/AlignMolecules.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend.internal". Scanning dependencies of target testOptimizer make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 22%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer/testOptimizer.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 22%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.h:15, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 22%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/SLNAttribs.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 22%] Built target rdPartialCharges make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/depend.internal". Scanning dependencies of target ForceField make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 22%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/ForceField.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 22%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 22%] Built target Subgraphs [ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmartsWrite.cpp [ 22%] Linking CXX executable testOptimizer cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 22%] Built target testOptimizer [ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/CXSmilesOps.cpp [ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Edge.cpp [ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o cd 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/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Configuration.cpp [ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp [ 22%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o cd /build/reproducible-path/rdkit-202009.4/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 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../../../lib/libRDKitMolAlign.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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Scanning dependencies of target Depictor make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 22%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/BondStretch.cpp [ 23%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so cd /build/reproducible-path/rdkit-202009.4/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 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Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 23%] Built target rdMolTransforms 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/CoordGen/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/CoordGen/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake --color= 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /build/reproducible-path/rdkit-202009.4/External/CoordGen/Wrap/rdCoordGen.cpp [ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/smiles.tab.cpp [ 23%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /build/reproducible-path/rdkit-202009.4/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 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp [ 23%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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'/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 24%] Built target rdMolCatalog [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202009.4/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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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 library ../../../lib/libRDKitMolInterchange.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 24%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/sln.tab.cpp cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2020.09.4 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 24%] Built target MolInterchange make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend.internal". 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-I/usr/include/rapidjson -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule2.cpp [ 24%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so -lpthread [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule3.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 24%] Built target rdtrajectory [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp [ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/Nonbonded.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp [ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/lex.yysmarts.cpp [ 25%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 25%] Built target rdqueries [ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/Inversion.cpp [ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/External/CoordGen/Wrap/rdCoordGen.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202009.4/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-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule6.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/TorsionAngle.cpp [ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp [ 27%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/lex.yysmiles.cpp [ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/DistanceConstraint.cpp [ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/AngleConstraint.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/TorsionConstraint.cpp [ 27%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/lex.yysln.cpp [ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/PositionConstraint.cpp [ 27%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/EmbeddedFrag.cpp [ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/Params.cpp [ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/AngleBend.cpp [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/BondStretch.cpp In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Conformer.h:14, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ROMol.h:36, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp:13: /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h: In function 'boost::python::tuple RDKit::getUnionOfTwoBox(boost::python::tuple, boost::python::tuple)': /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:31: warning: '*((void*)(&)+12).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:43: warning: '*((void*)(&)+12).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:55: warning: '*((void*)(&)+12).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:31: warning: '*((void*)(&)+12).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:43: warning: '*((void*)(&)+12).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:55: warning: '*((void*)(&)+12).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:31: warning: '*((void*)(&)+12).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:43: warning: '*((void*)(&)+12).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:55: warning: '*((void*)(&)+12).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:31: warning: '*((void*)(&)+12).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:43: warning: '*((void*)(&)+12).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:55: warning: '*((void*)(&)+12).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS 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Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/OopBend.cpp [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/TorsionAngle.cpp [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/Nonbonded.cpp [ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 [ 28%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so cd /build/reproducible-path/rdkit-202009.4/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 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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 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o ../../../lib/libRDKitCIPLabeler.so.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 28%] Built target rdMolInterchange [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp [ 28%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so -lpthread make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/AngleConstraint.cpp [ 28%] Built target rdCoordGen [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/TorsionConstraint.cpp [ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 28%] Built target rdShapeHelpers [ 28%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/DepictUtils.cpp [ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/PositionConstraint.cpp [ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/Params.cpp [ 29%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 29%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2020.09.4 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 29%] Built target SLNParse make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend.internal". Scanning dependencies of target rdSLNParse make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 29%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 29%] Built target SmilesParse make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend.internal". Scanning dependencies of target graphmolcpTest Scanning dependencies of target graphmolqueryTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build Scanning dependencies of target ChemTransforms make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 29%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o [ 29%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/querytest.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/cptest.cpp [ 29%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms/ChemTransforms.cpp [ 29%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms/MolFragmenter.cpp make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend.internal". Scanning dependencies of target graphmolMemTest1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 29%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/memtest1.cpp 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/depend.internal". Scanning dependencies of target test-valgrind make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 29%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/test-valgrind.cpp make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend.internal". Scanning dependencies of target graphmolIterTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 29%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/itertest.cpp make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend.internal". Scanning dependencies of target smaTest1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 29%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/smatest.cpp 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend.internal". Scanning dependencies of target smiTest2 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 29%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/smiTest2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/test2.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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend.internal". Scanning dependencies of target Fingerprints make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 29%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Fingerprints.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 29%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 29%] Built target rdCIPLabeler make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend.internal". 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend.internal". Scanning dependencies of target testSubgraphs1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 32%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSubgraphs1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs/test1.cpp [ 32%] Linking CXX executable test-valgrind cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 32%] Linking CXX executable graphmolMemTest1 cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 32%] Built target test-valgrind make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend.internal". make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 32%] Built target graphmolMemTest1 make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend Scanning dependencies of target FragCatalog make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake --color= [ 32%] Linking CXX shared library ../../../lib/libRDKitDepictor.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2020.09.4 /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.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend.internal". [ 32%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp Scanning dependencies of target testPartialCharges make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 32%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/test1.cpp [ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 33%] Built target Depictor make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend.internal". Scanning dependencies of target MolChemicalFeatures make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 33%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp [ 33%] Built target rdSLNParse make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend.internal". Scanning dependencies of target testCIPLabeler make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 33%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/catch_tests.cpp [ 33%] Linking CXX shared library ../../lib/libRDKitForceField.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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.1.2020.09.4 ../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2020.09.4 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 33%] Built target ForceField 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend.internal". Scanning dependencies of target ReducedGraphs make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 33%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DReducedGraphs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp [ 33%] Linking CXX executable graphmolIterTest cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 33%] Built target graphmolIterTest make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend.internal". Scanning dependencies of target testSLNParse make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 33%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/test.cpp [ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/PatternFingerprints.cpp [ 34%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp [ 34%] Linking CXX executable testPartialCharges cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPartialCharges.dir/test1.cpp.o -o testPartialCharges ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 34%] Linking CXX executable testSubgraphs2 cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 [ 34%] Built target testPartialCharges make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubgraphs2.dir/test2.cpp.o -o testSubgraphs2 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend.internal". 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Scanning dependencies of target rdchem make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 34%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/rdchem.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rdchem.cpp [ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganFingerprints.cpp [ 34%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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[ 34%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitReducedGraphs.so.1.2020.09.4 ../../../lib/libRDKitReducedGraphs.so.1 ../../../lib/libRDKitReducedGraphs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 34%] Built target ReducedGraphs 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend.internal". Scanning dependencies of target testReducedGraphs make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 34%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs/test1.cpp [ 34%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/Builder.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 34%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.cpp [ 34%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations/AbbreviationsUtils.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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 34%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp [ 34%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp [ 35%] Linking CXX executable testReducedGraphs cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 35%] 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend.internal". 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../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 36%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 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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-202009.4/obj-i686-linux-gnu' [ 36%] Built target smaTest1 [ 36%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp [ 36%] Linking CXX executable testSLNParse cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 36%] Built target testSLNParse [ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.cpp [ 36%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragFPGenerator.cpp [ 36%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 36%] Built target FilterCatalog make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend.internal". Scanning dependencies of target rdfiltercatalog make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 36%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp [ 36%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 36%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 36%] Built target rdReducedGraphs [ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp [ 36%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2020.09.4 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 36%] Built target MolChemicalFeatures make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend.internal". Scanning dependencies of target rdMolChemicalFeatures make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 37%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp [ 37%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairGenerator.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:31: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 37%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.cpp [ 37%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.h:36, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp [ 38%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp [ 38%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolFileStereochem.cpp [ 39%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 40%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2020.09.4 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 40%] Built target FragCatalog [ 41%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolFileWriter.cpp [ 41%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp [ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintUtil.cpp [ 41%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp [ 42%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Table.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Table.cpp [ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function 'std::string RDKit::SGroupWriting::BuildV2000SAPLines(int, const RDKit::SubstanceGroup&)': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: '%3d' directive output may be truncated writing between 3 and 11 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-2147483647, 2147483647] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/streambuf:41, from /usr/include/c++/10/bits/streambuf_iterator.h:35, from /usr/include/c++/10/iterator:66, from /usr/include/boost/iterator/iterator_traits.hpp:10, from /usr/include/boost/range/mutable_iterator.hpp:23, from /usr/include/boost/range/iterator.hpp:20, from /usr/include/boost/range/begin.hpp:20, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 5 and 13 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 43%] Built target rdAbbreviations [ 43%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Atom.cpp [ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SDMolSupplier.cpp [ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SDWriter.cpp In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function 'std::string RDKit::SGroupWriting::BuildV2000STYLines(const RDKit::ROMol&)': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: '%3d' directive output may be truncated writing between 3 and 9 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-23342212, 23342214] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/streambuf:41, from /usr/include/c++/10/bits/streambuf_iterator.h:35, from /usr/include/c++/10/iterator:66, from /usr/include/boost/iterator/iterator_traits.hpp:10, from /usr/include/boost/range/mutable_iterator.hpp:23, from /usr/include/boost/range/iterator.hpp:20, from /usr/include/boost/range/begin.hpp:20, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 5 and 11 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function 'std::string RDKit::SGroupWriting::BuildV2000SBTLines(const RDKit::ROMol&)': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: '%3d' directive output may be truncated writing between 3 and 9 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-23342212, 23342214] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/streambuf:41, from /usr/include/c++/10/bits/streambuf_iterator.h:35, from /usr/include/c++/10/iterator:66, from /usr/include/boost/iterator/iterator_traits.hpp:10, from /usr/include/boost/range/mutable_iterator.hpp:23, from /usr/include/boost/range/iterator.hpp:20, from /usr/include/boost/range/begin.hpp:20, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 5 and 11 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: '%3d' directive output may be truncated writing between 3 and 9 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-23342212, 23342214] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/streambuf:41, from /usr/include/c++/10/bits/streambuf_iterator.h:35, from /usr/include/c++/10/iterator:66, from /usr/include/boost/iterator/iterator_traits.hpp:10, from /usr/include/boost/range/mutable_iterator.hpp:23, from /usr/include/boost/range/iterator.hpp:20, from /usr/include/boost/range/begin.hpp:20, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 5 and 11 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function 'std::string RDKit::SGroupWriting::BuildV2000SDSLines(const RDKit::ROMol&)': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: '%3d' directive output may be truncated writing between 3 and 9 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-23342212, 23342214] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/streambuf:41, from /usr/include/c++/10/bits/streambuf_iterator.h:35, from /usr/include/c++/10/iterator:66, from /usr/include/boost/iterator/iterator_traits.hpp:10, from /usr/include/boost/range/mutable_iterator.hpp:23, from /usr/include/boost/range/iterator.hpp:20, from /usr/include/boost/range/begin.hpp:20, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 5 and 11 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function 'std::string RDKit::SGroupWriting::BuildV2000StringPropLines(unsigned int, const RDKit::ROMol&, const string&, const string&, unsigned int)': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: '%3d' directive output may be truncated writing between 3 and 9 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-23342212, 23342214] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/streambuf:41, from /usr/include/c++/10/bits/streambuf_iterator.h:35, from /usr/include/c++/10/iterator:66, from /usr/include/boost/iterator/iterator_traits.hpp:10, from /usr/include/boost/range/mutable_iterator.hpp:23, from /usr/include/boost/range/iterator.hpp:20, from /usr/include/boost/range/begin.hpp:20, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 5 and 11 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SmilesMolSupplier.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function 'std::string RDKit::SGroupWriting::BuildV2000SNCLines(const RDKit::ROMol&)': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: '%3d' directive output may be truncated writing between 3 and 9 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-23342212, 23342214] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/streambuf:41, from /usr/include/c++/10/bits/streambuf_iterator.h:35, from /usr/include/c++/10/iterator:66, from /usr/include/boost/iterator/iterator_traits.hpp:10, from /usr/include/boost/range/mutable_iterator.hpp:23, from /usr/include/boost/range/iterator.hpp:20, from /usr/include/boost/range/begin.hpp:20, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 5 and 11 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function 'std::string RDKit::SGroupWriting::BuildV2000SLBLines(const RDKit::ROMol&)': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: '%3d' directive output may be truncated writing between 3 and 9 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-23342212, 23342214] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/streambuf:41, from /usr/include/c++/10/bits/streambuf_iterator.h:35, from /usr/include/c++/10/iterator:66, from /usr/include/boost/iterator/iterator_traits.hpp:10, from /usr/include/boost/range/mutable_iterator.hpp:23, from /usr/include/boost/range/iterator.hpp:20, from /usr/include/boost/range/begin.hpp:20, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 5 and 11 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function 'std::string RDKit::SGroupWriting::BuildV2000SPLLines(const RDKit::ROMol&)': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: '%3d' directive output may be truncated writing between 3 and 9 bytes into a region of size 4 [-Wformat-truncation=] 24 | snprintf(output, 5, " %3d", value); | ^~~ /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:23: note: directive argument in the range [-23342212, 23342214] 24 | snprintf(output, 5, " %3d", value); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/streambuf:41, from /usr/include/c++/10/bits/streambuf_iterator.h:35, from /usr/include/c++/10/iterator:66, from /usr/include/boost/iterator/iterator_traits.hpp:10, from /usr/include/boost/range/mutable_iterator.hpp:23, from /usr/include/boost/range/iterator.hpp:20, from /usr/include/boost/range/begin.hpp:20, from /usr/include/boost/algorithm/string/detail/sequence.hpp:17, from /usr/include/boost/algorithm/string/join.hpp:15, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:11: /usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 5 and 11 bytes into a destination of size 5 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 43%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp [ 43%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 43%] Built target ForceFieldHelpers make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= [ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/depend.internal". cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SmilesWriter.cpp Scanning dependencies of target DistGeometry make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 43%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/TDTMolSupplier.cpp [ 43%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 43%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Bond.cpp [ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/TDTWriter.cpp [ 43%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/TplFileParser.cpp cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 44%] Built target Fingerprints 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend.internal". Scanning dependencies of target rdForceField make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 44%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/Wrap/ForceField.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/TplFileWriter.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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend.internal". Scanning dependencies of target rdMHFPFingerprint make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 44%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend.internal". Scanning dependencies of target rdFingerprintGenerator make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 45%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/PDBParser.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 45%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DistGeom/TriangleSmooth.cpp 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend.internal". Scanning dependencies of target rdForceFieldHelpers make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 45%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/PDBWriter.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-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/PDBSupplier.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/XYZFileWriter.cpp [ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 45%] Built target rdMolChemicalFeatures make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend.internal". Scanning dependencies of target O3AAlign make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 45%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp [ 45%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DistGeom/DistViolationContrib.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MaeMolSupplier.cpp [ 45%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPMol.cpp /build/reproducible-path/rdkit-202009.4/Code/ForceField/Wrap/ForceField.cpp: In member function 'double ForceFields::PyForceField::calcEnergyWithPos(const boost::python::api::object&)': /build/reproducible-path/rdkit-202009.4/Code/ForceField/Wrap/ForceField.cpp:136:12: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 136 | c[i] = python::extract(pos[i]); /build/reproducible-path/rdkit-202009.4/Code/ForceField/Wrap/ForceField.cpp: In member function 'PyObject* ForceFields::PyForceField::calcGradWithPos(const boost::python::api::object&)': /build/reproducible-path/rdkit-202009.4/Code/ForceField/Wrap/ForceField.cpp:172:12: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 172 | c[i] = python::extract(pos[i]); [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/ProximityBonds.cpp [ 46%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DistGeom/ChiralViolationContrib.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK 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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++11 -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SequenceWriters.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SVGParser.cpp [ 47%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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.1.2020.09.4 ../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../lib/libRDKitForceField.so.1.2020.09.4 ../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 47%] Built target DistGeometry 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary 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Scanning dependencies of target SubstructLibrary make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 47%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/PNGParser.cpp [ 47%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPLabeler.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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/Conformer.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Conformer.cpp [ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 47%] Built target rdForceFieldHelpers [ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/RingInfo.cpp [ 47%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 47%] Built target rdForceField 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend.internal". Scanning dependencies of target DistGeomHelpers make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 47%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp [ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so cd 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../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 47%] Built target rdFingerprintGenerator make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/depend.internal". Scanning dependencies of target testDistGeom make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 47%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DistGeom/testDistGeom.cpp [ 47%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend.internal". 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Scanning dependencies of target DistGeom make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 48%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DistGeom/Wrap/DistGeom.cpp cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2020.09.4 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 48%] Built target O3AAlign [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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/rdMHFPFingerprint.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 48%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Mancude.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 48%] Built target rdMHFPFingerprint [ 48%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Digraph.cpp [ 49%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 49%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Node.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 49%] Built target rdfiltercatalog [ 50%] Linking CXX executable testDistGeom cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 [ 51%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Edge.cpp /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../lib/libRDKitForceField.so.1.2020.09.4 ../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 51%] Built target testDistGeom [ 51%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Sort.cpp [ 51%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Configuration.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 51%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp [ 51%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp [ 51%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include 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-I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MonomerInfo.cpp [ 51%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o cd /build/reproducible-path/rdkit-202009.4/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 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Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp [ 52%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 52%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/PatternFactory.cpp [ 53%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5.cpp [ 53%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp [ 53%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule6.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/EditableMol.cpp:17: /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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 53%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Conformer.cpp:21: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ [ 53%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/StereoGroup.cpp [ 53%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SubstanceGroup.cpp [ 53%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Chirality.cpp [ 53%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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/XYZFileWriter.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.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /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.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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-202009.4/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-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1 ../../../lib/libRDKitFileParsers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 53%] 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/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/UFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/UFF/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/CoordGen/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend.internal". Scanning dependencies of target graphmolAdjustQueryCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 53%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_adjustquery.cpp Scanning dependencies of target testUFFForceField Scanning dependencies of target testCoordGen make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 53%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o [ 54%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/testUFFForceField.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCoordGen.dir/test.cpp.o -c /build/reproducible-path/rdkit-202009.4/External/CoordGen/test.cpp [ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_main.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_main.cpp [ 56%] Linking CXX executable testCIPLabeler cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 56%] Built target testCIPLabeler make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend.internal". Scanning dependencies of target graphmolSGroupCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 56%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_sgroups.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake --color= /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend.internal". Scanning dependencies of target graphmolTestsCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 56%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_graphmol.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-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 57%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2020.09.4 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 57%] Built target SubstructLibrary make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend.internal". Scanning dependencies of target chiralityTestsCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 57%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_chirality.cpp make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend.internal". Scanning dependencies of target graphmolTest1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 57%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/test1.cpp [ 57%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 57%] Built target DistGeomHelpers make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/depend.internal". Scanning dependencies of target hanoiTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 57%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/hanoitest.cpp make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/depend.internal". Scanning dependencies of target testSGroup make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 57%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/testSGroup.cpp make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend.internal". Scanning dependencies of target graphmoltestPicklerGlobalSetting make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 57%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/testPicklerGlobalSettings.cpp make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend.internal". Scanning dependencies of target graphmolMolOpsTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 57%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/molopstest.cpp [ 57%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_main.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/chiralityTestsCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_main.cpp [ 57%] Linking CXX executable testUFFForceField cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 57%] Built target testUFFForceField make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend.internal". Scanning dependencies of target graphmoltestChirality make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Conformer.h:14, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RDKitBase.h:25, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SubstanceGroup.cpp:17: /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h: In function 'void RDKit::{anonymous}::addBracketHelper(RDKit::SubstanceGroup&, boost::python::api::object)': /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:31: warning: '*((void*)(&)+12).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:43: warning: '*((void*)(&)+12).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:55: warning: '*((void*)(&)+12).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ [ 57%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/testChirality.cpp [ 57%] Linking CXX executable testCoordGen cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /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.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl -lpthread make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 57%] Built target testCoordGen make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend.internal". Scanning dependencies of target graphmoltestPickler make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 57%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/testPickler.cpp make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/depend.internal". Scanning dependencies of target molBundleTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 58%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/testMolBundle.cpp [ 58%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_main.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolSGroupCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_main.cpp make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend.internal". Scanning dependencies of target resMolSupplierTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 58%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/resMolSupplierTest.cpp [ 58%] Linking CXX executable hanoiTest cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 58%] Built target hanoiTest make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend.internal". 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Scanning dependencies of target testDepictor make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 58%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/testDepictor.cpp [ 58%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 58%] Built target rdchem make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend.internal". Scanning dependencies of target cxsmilesTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 59%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/cxsmiles_test.cpp [ 59%] Linking CXX executable graphmoltestPicklerGlobalSetting cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 59%] Built target graphmoltestPicklerGlobalSetting make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend.internal". Scanning dependencies of target smiTestCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 59%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/catch_tests.cpp [ 59%] Linking CXX executable molBundleTest cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 59%] Built target molBundleTest 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend.internal". 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-I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/smiTest1.dir/test.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/test.cpp [ 59%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_main.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolTestsCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_main.cpp [ 59%] Linking CXX executable graphmolTest1 cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../lib/libRDKitForceField.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl -lpthread make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 59%] Built target graphmolTest1 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend.internal". Scanning dependencies of target testMol2ToMol make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testMol2ToMol.cpp [ 60%] Linking CXX executable resMolSupplierTest cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 60%] Built target resMolSupplierTest 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend.internal". Scanning dependencies of target fileParsersTest1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/test1.cpp [ 60%] Linking CXX executable testSGroup cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend.internal". Scanning dependencies of target testPropertyLists make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testPropertyLists.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 60%] Built target testSGroup 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend.internal". Scanning dependencies of target testMolSupplier make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testMolSupplier.cpp [ 60%] Linking CXX executable testMol2ToMol cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 60%] Built target testMol2ToMol 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend.internal". Scanning dependencies of target testGeneralFileReader make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testGeneralFileReader.cpp /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testMolSupplier.cpp: In function 'void testGitHub3517()': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testMolSupplier.cpp:2805:10: warning: unused variable 'l' [-Wunused-variable] 2805 | size_t l = sdsup.length(); | ^ [ 60%] Linking CXX executable testDepictor cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /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/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 60%] Built target testDepictor 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend.internal". Scanning dependencies of target testSequence make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testSequence.cpp [ 61%] Linking CXX executable cxsmilesTest cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 61%] Built target cxsmilesTest 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend.internal". Scanning dependencies of target testMolWriter make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testMolWriter.cpp [ 62%] Linking CXX executable testSequence cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 62%] Built target testSequence 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend.internal". Scanning dependencies of target testTplParser make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testTpls.cpp [ 63%] Linking CXX executable testGeneralFileReader cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitRDStreams.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -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 -lpthread /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 63%] Built target testGeneralFileReader 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend.internal". Scanning dependencies of target testExtendedStereoParsing make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp [ 64%] Linking CXX executable graphmoltestPickler cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 64%] Built target graphmoltestPickler 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend.internal". Scanning dependencies of target testMultithreadedMolSupplier make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 64%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp [ 64%] Linking CXX executable graphmoltestChirality cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 64%] Built target graphmoltestChirality 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend.internal". Scanning dependencies of target fileParsersCatchTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 64%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/file_parsers_catch.cpp [ 64%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/catch_main.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testPropertyLists.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/catch_main.cpp [ 64%] Linking CXX executable testTplParser cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 64%] Built target testTplParser make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend.internal". Scanning dependencies of target substructTestCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 64%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct/catch_tests.cpp [ 65%] Linking CXX executable testExtendedStereoParsing cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 65%] 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend.internal". Scanning dependencies of target testSubstructMatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 65%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct/test1.cpp [ 65%] Linking CXX executable graphmolAdjustQueryCatch cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 CMakeFiles/graphmolAdjustQueryCatch.dir/catch_main.cpp.o -o graphmolAdjustQueryCatch ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 65%] Built target graphmolAdjustQueryCatch 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend.internal". Scanning dependencies of target Descriptors make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/Crippen.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Crippen.cpp [ 65%] Linking CXX executable testMultithreadedMolSupplier cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitRDStreams.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl -lpthread /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 65%] Built target testMultithreadedMolSupplier make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend.internal". 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend.internal". Scanning dependencies of target filterCatalogTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 65%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp [ 65%] Linking CXX executable testMolWriter cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 65%] Built target testMolWriter make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend.internal". 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Scanning dependencies of target testFragCatalog make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 65%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/test1.cpp [ 65%] Linking CXX executable graphmolSGroupCatch [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o cd /build/reproducible-path/rdkit-202009.4/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 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--verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 CMakeFiles/graphmolSGroupCatch.dir/catch_main.cpp.o -o graphmolSGroupCatch ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 65%] Built target graphmolSGroupCatch 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap 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Scanning dependencies of target rdfragcatalog make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 65%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp [ 65%] Linking CXX executable filterCatalogTest cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 65%] Built target filterCatalogTest 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend.internal". Scanning dependencies of target fpTestCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 65%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/catch_tests.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.h:15, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 65%] Linking CXX executable testSubstructMatch cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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 [ 65%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 65%] Built target testSubstructMatch 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend.internal". 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Scanning dependencies of target testFingerprints make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 65%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/test1.cpp [ 66%] Linking CXX executable graphmolTestsCatch cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 CMakeFiles/graphmolTestsCatch.dir/catch_main.cpp.o -o graphmolTestsCatch ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 [ 66%] Linking CXX executable smiTest1 cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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 [ 66%] Linking CXX executable testFragCatalog cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 66%] Built target graphmolTestsCatch 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend.internal". [ 66%] Built target smiTest1 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake --color= Scanning dependencies of target testFingerprintGenerators make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend.internal". Scanning dependencies of target testMHFPFingerprint make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 66%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp [ 66%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 66%] Built target testFragCatalog make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend.internal". Scanning dependencies of target testMolTransforms make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 66%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms/test1.cpp [ 66%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/catch_main.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/fileParsersCatchTest.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/catch_main.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MolDescriptors.cpp [ 66%] Linking CXX executable testChemTransforms cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 66%] Built target testChemTransforms 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend.internal". Scanning dependencies of target testMMFFForceFieldHelpersMultiThread make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 66%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp [ 66%] Linking CXX executable testMHFPFingerprint cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend.internal". Scanning dependencies of target testMMFFForceFieldHelpers make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 66%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp [ 66%] Linking CXX executable testMolTransforms cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 66%] Built target testMolTransforms 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend.internal". Scanning dependencies of target testUFFForceFieldHelpers make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 66%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp [ 67%] Linking CXX executable fileParsersTest1 cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 67%] Built target fileParsersTest1 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend.internal". Scanning dependencies of target testCrystalForceField make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 67%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp [ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MolSurf.cpp [ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp [ 67%] Linking CXX executable testMMFFForceFieldHelpersMultiThread cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 67%] Built target testMMFFForceFieldHelpersMultiThread 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend.internal". Scanning dependencies of target testDistGeomHelpers make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 67%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragCatParams.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o [ 67%] Linking CXX executable testCrystalForceField cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Lipinski.cpp cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 67%] 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend.internal". 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp [ 69%] Linking CXX executable testFingerprintGenerators cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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/usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so [ 69%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 69%] Built target testFingerprintGenerators 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E 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Scanning dependencies of target testShapeHelpers make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 69%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp [ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp [ 69%] Linking CXX executable testUFFForceFieldHelpers cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 69%] Built target testUFFForceFieldHelpers 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend.internal". Scanning dependencies of target testMolCatalog make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 69%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/test1.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 69%] Linking CXX executable testFingerprints cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 69%] Built target testFingerprints make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend.internal". Scanning dependencies of target FMCS make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 69%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/FMCS.cpp [ 69%] Linking CXX executable testShapeHelpers cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 69%] Built target testShapeHelpers [ 69%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Seed.cpp [ 70%] Linking CXX executable graphmolMolOpsTest cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 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-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 70%] Built target graphmolMolOpsTest make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend.internal". 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Scanning dependencies of target MMPA make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 70%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA/MMPA.cpp [ 70%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp [ 70%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MQN.cpp [ 70%] Linking CXX executable testFeatures cd 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Scanning dependencies of target substructLibraryTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 71%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp [ 72%] Linking CXX executable testMolCatalog cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 72%] Built target testMolCatalog 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend.internal". 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Scanning dependencies of target rdSubstructLibrary make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 72%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202009.4/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/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Property.cpp [ 73%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp [ 73%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /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/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 73%] Built target rdDistGeom make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend make[4]: Entering directory 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend.internal". Scanning dependencies of target molInterchangeTest1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 74%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/rapidjson -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/test1.cpp [ 74%] Linking CXX executable testDistGeomHelpers cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 74%] 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend.internal". Scanning dependencies of target rdmolfiles make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rdmolfiles.cpp [ 74%] Linking CXX shared library ../../../lib/libRDKitMMPA.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2020.09.4 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 74%] Built target MMPA make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend.internal". 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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.h:36, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ Scanning dependencies of target testAbbreviations make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 74%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/__/catch_main.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -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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-I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp [ 74%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 [ 74%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS && 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations/catch_tests.cpp [ 75%] Linking CXX executable trajectoryTest cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/MMFF/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend.internal". Scanning dependencies of target testMMFFForceField make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 75%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/testMMFFForceField.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 75%] Linking CXX executable fileParsersCatchTest cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 CMakeFiles/fileParsersCatchTest.dir/catch_main.cpp.o -o fileParsersCatchTest ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 75%] Built target fileParsersCatchTest 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend.internal". 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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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 75%] Linking CXX executable substructLibraryTest cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 75%] Built target substructLibraryTest 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend.internal". 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Scanning dependencies of target rdMMPA make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 76%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:34: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ [ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ 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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. 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/PBF.cpp [ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/PMI.cpp /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:186:56: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:156:58: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ [ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/AUTOCORR3D.cpp [ 79%] Linking CXX shared library ../../../lib/libRDKitFMCS.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 79%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:404:16: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 404 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 79%] Built target rdMMPA [ 79%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SDMolSupplier.cpp cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 79%] 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend.internal". Scanning dependencies of target testFMCS make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 79%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202009.4/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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/RDF.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/RDF.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:22: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MaeMolSupplier.cpp:22: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ [ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MORSE.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MORSE.cpp [ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o cd 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-std=gnu++11 -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/GETAWAY.cpp [ 79%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 79%] Linking CXX executable fpTestCatch cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:186:56: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:156:58: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 79%] Built target rdSubstructLibrary 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend.internal". 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-I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/FMCStest.dir/testFMCS.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Test/testFMCS.cpp [ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/CoulombMat.cpp /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:404:16: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 404 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:186:56: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:156:58: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ [ 79%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o [ 79%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -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/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:404:16: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 404 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 79%] Linking CXX executable substructTestCatch cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. 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/usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.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-202009.4/obj-i686-linux-gnu' [ 79%] Built target testMMFFForceField 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp [ 79%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SmilesWriter.cpp /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/GETAWAY.cpp: In function 'Eigen::MatrixXd RDKit::Descriptors::{anonymous}::GetPinv(const MatrixXd&)': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/GETAWAY.cpp:285:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'Eigen::Index' {aka 'int'} [-Wsign-compare] 285 | for (unsigned int i = 0; i < A.cols(); ++i) { | ~~^~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'std::string testChEMBL_Txt(const char*, double, const char*)': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Test/testFMCS.cpp:545:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 545 | 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-202009.4/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet_SMI(const char*, const char*)': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Test/testFMCS.cpp:1226:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 1226 | 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-202009.4/Code/GraphMol/FMCS/Test/testFMCS.cpp:1238:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 1238 | 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-202009.4/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet(const char*, const char*)': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Test/testFMCS.cpp:1343:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 1343 | 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-202009.4/Code/GraphMol/FMCS/Test/testFMCS.cpp:1396:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 1396 | 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-202009.4/Code/GraphMol/FMCS/Test/testFMCS.cpp:1484:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 1484 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u [ 79%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SDWriter.cpp [ 79%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/TDTWriter.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/PDBWriter.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/TDTMolSupplier.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SmilesMolSupplier.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, 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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SmilesWriter.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SDWriter.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, 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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/TDTWriter.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 80%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SmilesWriter.cpp:20: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/TDTWriter.cpp:21: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SDWriter.cpp:21: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ 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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/PDBWriter.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 80%] Linking CXX executable testFMCS cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 80%] Built target testFMCS [ 80%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupScore.cpp [ 80%] Linking CXX executable FMCStest cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 80%] Built target FMCStest [ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/PDBWriter.cpp:20: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ [ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:186:56: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:156:58: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:186:56: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:156:58: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:186:56: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:156:58: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:404:16: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 404 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:404:16: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 404 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:404:16: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 404 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:186:56: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:156:58: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:404:16: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 404 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedMolSupplier.h:15, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp:23: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedMolSupplier.h:15, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp:23: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ [ 81%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o ../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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 cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2020.09.4 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 81%] Built target RGroupDecomposition make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition 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"/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend.internal". Scanning dependencies of target testRGroupDecomp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Scanning dependencies of target rdRGroupDecomposition [ 81%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 81%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp [ 81%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2020.09.4 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/usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 81%] Built target rdFMCS [ 81%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /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/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so -lpthread make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 81%] Built target rdmolfiles 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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp:47: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ [ 81%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 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../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 81%] Built target Descriptors make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend make -f 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/depend.internal". Scanning dependencies of target testAUTOCORR3D Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend.internal". make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build Scanning dependencies of target testAUTOCORR2D Scanning dependencies of target testRDF Scanning dependencies of target testRDFcustom Scanning dependencies of target testBCUT make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Scanning dependencies of target testATF make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend.internal". make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Scanning dependencies of target test3D make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Scanning dependencies of target testEEM make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Scanning dependencies of target testDescriptors make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build Scanning dependencies of target testPBF make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Scanning dependencies of target testCoulombMat make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build [ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/testAUTOCORR3D.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/testRDF.cpp.o [ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o [ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testRDF.dir/testRDF.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/testRDF.cpp [ 82%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/testBCUT.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/testRDFcustom.cpp [ 82%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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Scanning dependencies of target testWHIM make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 83%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include 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../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend.internal". 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-I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/testO3AAlign.cpp [ 83%] Linking CXX executable testAUTOCORR3D cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR3D.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 83%] Linking CXX executable testRDF cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 83%] Built target testAUTOCORR3D make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend.internal". [ 84%] Linking CXX executable testAUTOCORR2D cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl Scanning dependencies of target testMolAlign make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 84%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/testMolAlign.cpp [ 84%] Built target testRDF make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend.internal". Scanning dependencies of target rdMolAlign make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 84%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 84%] Built target testAUTOCORR2D 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend.internal". Scanning dependencies of target MolHash make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 84%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/hashfunctions.cpp [ 84%] Linking CXX executable testCoulombMat cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 /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/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 84%] Built target testCoulombMat [ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/MDLParser.cpp [ 84%] Linking CXX executable testPBF cd 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[ 84%] Built target testPBF [ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionPickler.cpp [ 84%] Linking CXX executable testEEM cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEEM.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testEEM.dir/testEEM.cpp.o -o testEEM ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory 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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++11 -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionWriter.cpp [ 84%] Linking CXX executable testRDFcustom cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDFcustom.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -o testRDFcustom 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../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 84%] Built target testRDFcustom [ 85%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/normalize.cpp [ 85%] Linking CXX executable test3D cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/test3D.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/test3D.dir/test3D.cpp.o -o test3D ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 85%] Built target test3D [ 85%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionDepict.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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 85%] Linking CXX executable testMORSE cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMORSE.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMORSE.dir/testMORSE.cpp.o -o testMORSE ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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-202009.4/obj-i686-linux-gnu' [ 85%] Built target testMORSE [ 85%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp [ 85%] Linking CXX executable testGETAWAY cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGETAWAY.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -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/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 85%] Built target testGETAWAY [ 85%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionUtils.cpp [ 85%] Linking CXX executable testWHIM cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testWHIM.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testWHIM.dir/testWHIM.cpp.o -o testWHIM ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /build/reproducible-path/rdkit-202009.4/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-202009.4/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:478:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] 478 | (python::len(prbCrippenContribs) == prbNAtoms)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:493:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] 493 | (python::len(refCrippenContribs) == refNAtoms)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/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-202009.4/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:559:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] 559 | (python::len(prbCrippenContribs) == prbNAtoms)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:574:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] 574 | (python::len(refCrippenContribs) == refNAtoms)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 85%] Built target testWHIM [ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/MoleculeParser.cpp [ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionRunner.cpp [ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/PreprocessRxn.cpp [ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/SanitizeRxn.cpp [ 86%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat 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/usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/PNGParser.cpp cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2020.09.4 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 86%] Built target MolHash 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake" is newer than depender 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend.internal". Scanning dependencies of target molHashCatchTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 86%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/catch_tests.cpp [ 86%] Linking CXX executable testMolAlign cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 /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.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 86%] Built target testMolAlign 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend.internal". Scanning dependencies of target rdMolHash make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 86%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp [ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp [ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp [ 86%] Linking CXX executable testO3AAlign cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 /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.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 86%] Built target testO3AAlign 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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp: In function 'boost::python::list {anonymous}::GetUSRFromDistributions(boost::python::api::object)': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:659:18: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 659 | tmpDist[j] = python::extract(distances[i][j]); In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:24: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Conformer.h:14, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ROMol.h:36, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/GraphMol.h:19, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:12: /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h: In function 'boost::python::list {anonymous}::GetUSRDistributionsFromPoints(boost::python::api::object, boost::python::api::object)': /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:87:15: warning: '*((void*)(&)+12).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] 87 | x = other.x; | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:88:15: warning: '*((void*)(&)+12).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] 88 | y = other.y; | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:89:15: warning: '*((void*)(&)+12).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] 89 | z = other.z; | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h: In function 'boost::python::list {anonymous}::GetUSRDistributions(boost::python::api::object, boost::python::api::object)': /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:87:15: warning: '*((void*)(&)+12).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] 87 | x = other.x; | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:88:15: warning: '*((void*)(&)+12).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] 88 | y = other.y; | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:89:15: warning: '*((void*)(&)+12).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] 89 | z = other.z; | ~~~~~~^ [ 86%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 86%] Built target rdMolHash [ 86%] Linking CXX executable testDescriptors cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDescriptors.dir/test.cpp.o -o testDescriptors ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 86%] Built target testDescriptors [ 86%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 /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/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 86%] Built target rdMolAlign [ 87%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 87%] 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/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake --color= make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake --color= 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake --color= 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend.internal". Scanning dependencies of target testReactionFingerprints Scanning dependencies of target testEnumeration Scanning dependencies of target Deprotect Scanning dependencies of target rxnTestCatch Scanning dependencies of target MolEnumerator Scanning dependencies of target testReaction Scanning dependencies of target rdChemReactions make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build 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-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 87%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o [ 87%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o [ 87%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect/Deprotect.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/testReaction.cpp [ 87%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o [ 87%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o [ 87%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp [ 87%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/catch_tests.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp [ 87%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o [ 88%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/LinkNode.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp [ 88%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/PositionVariation.cpp Scanning dependencies of target MolStandardize make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o [ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/MolStandardize.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Metal.cpp Scanning dependencies of target MolDraw2D make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202009.4/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/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-202009.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Normalize.cpp [ 89%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/Deprotect.dir/Deprotect.cpp.o ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202009.4/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:24, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.h:14, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2020.09.4 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 89%] Built target Deprotect [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Validate.cpp [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Charge.cpp [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Tautomer.cpp [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Fragment.cpp [ 90%] Linking CXX executable testReactionFingerprints cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 90%] Built target testReactionFingerprints 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect/deprotectTest.cpp [ 90%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolEnumerator.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/catch_main.cpp [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect/Wrap/rdDeprotect.h:15, from /build/reproducible-path/rdkit-202009.4/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/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp [ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o cd /build/reproducible-path/rdkit-202009.4/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 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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++11 -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp [ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp [ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o [ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202009.4/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 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-fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/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-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp [ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT 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-I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp [ 92%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security 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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++11 -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextJS.cpp [ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFT.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-202009.4/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:24, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:28, from /build/reproducible-path/rdkit-202009.4/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. 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-isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp [ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/enumerator_catch.cpp [ 94%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /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/libboost_serialization.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 94%] Built target MolStandardize make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend.internal". Scanning dependencies of target molStandardizeTest Scanning dependencies of target TautomerQuery make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 95%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/test1.cpp cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTautomerQuery_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery/TautomerQuery.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend.internal". Scanning dependencies of target molStandardizeSmallTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/test2.cpp [ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend.internal". Scanning dependencies of target molValidateTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molValidateTest.dir/testValidate.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/testValidate.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 95%] Built target rdChemReactions 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend.internal". Scanning dependencies of target molNormalizeTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/testNormalize.cpp 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend.internal". Scanning dependencies of target molChargeTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/testCharge.cpp [ 95%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 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/DrawText.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o ../../../lib/libRDKitChemReactions.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 95%] Built target MolDraw2D 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend.internal". Scanning dependencies of target molTautomerTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/testTautomer.cpp [ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 95%] Built target rdMolEnumerator 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake --color= Dependee 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend.internal". Scanning dependencies of target molFragmentTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/testFragment.cpp [ 95%] Linking CXX executable molStandardizeSmallTest cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 95%] Built target molStandardizeSmallTest 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend.internal". Scanning dependencies of target molStandardizeCatchTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/catch_tests.cpp [ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /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.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 95%] Built target rdMolDescriptors make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend.internal". Scanning dependencies of target rdMolStandardize make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 95%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp [ 95%] Linking CXX executable molValidateTest cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Validate.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 96%] Built target molValidateTest 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake --color= Dependee 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend.internal". Scanning dependencies of target ScaffoldNetwork make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 97%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DScaffoldNetwork_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp [ 97%] Linking CXX executable molNormalizeTest cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 97%] Built target molNormalizeTest 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend.internal". Scanning dependencies of target moldraw2DRxnTest1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 97%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/rxn_test1.cpp [ 97%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 97%] Linking CXX executable molStandardizeTest cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2020.09.4 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 97%] Built target TautomerQuery 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend.internal". Scanning dependencies of target moldraw2DTestCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 97%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_main.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/moldraw2DTestCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/catch_main.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 97%] Built target molStandardizeTest 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend.internal". Scanning dependencies of target moldraw2DTest1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 98%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/test1.cpp [ 98%] Linking CXX executable molChargeTest cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 98%] Built target molChargeTest make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend.internal". Scanning dependencies of target rdMolDraw2D make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 98%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202009.4/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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Linking CXX executable molHashCatchTest cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 ../../../lib/libRDKitMolHash.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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 molFragmentTest cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 98%] Built target molHashCatchTest [ 98%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/catch_tests.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 98%] Built target molFragmentTest 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend.internal". Scanning dependencies of target rdmolops make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 98%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rdmolops.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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 moldraw2DRxnTest1 cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/i386-linux-gnu/libfreetype.so [ 98%] Linking CXX executable testMolEnumerator cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/catch_main.cpp.o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../../lib/libRDKitMolEnumerator.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 98%] Built target moldraw2DRxnTest1 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend.internal". Scanning dependencies of target tautomerQueryTestCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 98%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery/catch_tests.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 98%] Built target testMolEnumerator 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend.internal". 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Scanning dependencies of target rdTautomerQuery make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 98%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdTautomerQuery_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp [ 98%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2020.09.4 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2020.09.4 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 98%] Built target ScaffoldNetwork 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend.internal". Scanning dependencies of target testScaffoldNetwork make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_main.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testScaffoldNetwork.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/catch_main.cpp [ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202009.4/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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MolOps.cpp make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend.internal". Scanning dependencies of target rdScaffoldNetwork make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' [ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdScaffoldNetwork_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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 deprotectTest cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 ../../../lib/libRDKitDeprotect.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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-202009.4/obj-i686-linux-gnu' [ 98%] Built target deprotectTest In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Conformer.h:14, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ROMol.h:36, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:17: /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = RDGeom::Point2D]': /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:269:57: warning: '*((void*)(&)+12).RDGeom::Point2D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] 269 | Point2D(const Point2D &other) : Point(other), x(other.x), y(other.y) {} | ~~~~~~^ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:269:69: warning: '*((void*)(&)+12).RDGeom::Point2D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] 269 | Point2D(const Point2D &other) : Point(other), x(other.x), y(other.y) {} | ~~~~~~^ [ 98%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/ChiralityOps.cpp In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:14: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = double]': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:120:9: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 120 | T v = python::extract(obj[i]); | ^ In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MolOps.cpp:30: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { | ~~^~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 297 | if ((!df_isTextMode || c <= STD_ASCII) && | ~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp: In function 'void RDKit::{anonymous}::pyDictToDoubleMap(boost::python::api::object, std::map&)': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:76:57: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 76 | double r = python::extract(tDict.values()[i]); | ^ [ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o [ 98%] Linking CXX executable molTautomerTest cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 98%] Built target molTautomerTest [ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp [ 98%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 98%] Built target rdTautomerQuery [ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Metal.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-202009.4/Code/RDBoost/python.h:3, from /build/reproducible-path/rdkit-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ /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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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-202009.4/Code/RDBoost/Wrap.h:20, from /build/reproducible-path/rdkit-202009.4/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:186:56: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 186 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:156:58: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | off_type py_pos = bp::extract(py_tell()); | ^ [ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp [ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202009.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp [ 98%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 98%] Built target rdScaffoldNetwork [ 98%] Linking CXX executable rxnTestCatch cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:404:16: warning: '*((void*)& +12)' may be used uninitialized in this function [-Wmaybe-uninitialized] 404 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Linking CXX executable testReaction cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 98%] Built target testReaction make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 98%] Built target rxnTestCatch [ 98%] Linking CXX executable moldraw2DTest1 cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/i386-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 98%] Built target moldraw2DTest1 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-202009.4/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( | ^~~~~~~~~~~~~~~~~~~~ [ 99%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /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.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libfreetype.so /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 99%] Built target rdMolDraw2D [ 99%] Linking CXX executable testScaffoldNetwork cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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_main.cpp.o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../../lib/libRDKitScaffoldNetwork.so.1.2020.09.4 ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 99%] Linking CXX executable moldraw2DTestCatch cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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_main.cpp.o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../lib/libRDKitCIPLabeler.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 99%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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/libRDKitMolDraw2D.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libfreetype.so /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 99%] Built target testScaffoldNetwork make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 99%] Built target rdmolops [ 99%] Built target moldraw2DTestCatch [ 99%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libpython3.9.so /usr/lib/i386-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 99%] Built target rdMolStandardize [100%] Linking CXX executable tautomerQueryTestCatch cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 ../../../lib/libRDKitTautomerQuery.so.1.2020.09.4 ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [100%] Built target tautomerQueryTestCatch [100%] Linking CXX executable molStandardizeCatchTest cd /build/reproducible-path/rdkit-202009.4/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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /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/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [100%] Built target molStandardizeCatchTest make[3]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' STATIC_LINK=0 RDKIT_LIBDIR=/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu//lib pg_buildext build /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit build-%v ### PostgreSQL 13 build ### make[2]: Entering directory '/build/reproducible-path/rdkit-202009.4/build-13' gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/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 -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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/mol_op.c /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function 'mol_murckoscaffold': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:263:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 263 | CROMol scaffold = MolMurckoScaffold(mol); | ^~~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function 'mol_nm_hash': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:283:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 283 | char *str = computeNMMolHash(mol, opts); | ^~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:285:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 285 | char *res = pnstrdup(str, strlen(str)); | ^~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:278:7: warning: unused variable 'len' [-Wunused-variable] 278 | int len; | ^~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function 'mol_adjust_query_properties': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:298:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 298 | char *data = PG_GETARG_CSTRING(1); | ^~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:304:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 304 | Mol *res = deconstructROMol(adj); | ^~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function 'mol_to_svg': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:319:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 319 | char *legend = PG_GETARG_CSTRING(1); | ^~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_smiles': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:343:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 343 | char *res = pnstrdup(str, strlen(str)); | ^~~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:34: /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mol2s_transition': /usr/include/postgresql/13/server/fmgr.h:268:29: warning: initialization of 'CROMol' {aka 'void *'} from 'Datum' {aka 'unsigned int'} makes pointer from integer without a cast [-Wint-conversion] 268 | #define PG_GETARG_DATUM(n) (fcinfo->args[n].value) | ^ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:395:18: note: in expansion of macro 'PG_GETARG_DATUM' 395 | CROMol mol = PG_GETARG_DATUM(1); | ^~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:411:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 411 | text *ts = (text *)palloc(ts_size); // new return value | ^~~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:34: /usr/include/postgresql/13/server/fmgr.h:268:29: warning: initialization of 'CROMol' {aka 'void *'} from 'Datum' {aka 'unsigned int'} makes pointer from integer without a cast [-Wint-conversion] 268 | #define PG_GETARG_DATUM(n) (fcinfo->args[n].value) | ^ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:423:18: note: in expansion of macro 'PG_GETARG_DATUM' 423 | CROMol mol = PG_GETARG_DATUM(1); | ^~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:431:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 431 | char *smiles = makeMolText(mol, &len, false, false); | ^~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mols': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:469:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 469 | int32 ts_size = VARHDRSZ + strlen(str); | ^~~~~ In file included from /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:34: /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mol_transition': /usr/include/postgresql/13/server/fmgr.h:268:29: warning: initialization of 'CROMol' {aka 'void *'} from 'Datum' {aka 'unsigned int'} makes pointer from integer without a cast [-Wint-conversion] 268 | #define PG_GETARG_DATUM(n) (fcinfo->args[n].value) | ^ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:491:18: note: in expansion of macro 'PG_GETARG_DATUM' 491 | CROMol mol = PG_GETARG_DATUM(1); | ^~~~~~~~~~~~~~~ /usr/include/postgresql/13/server/fmgr.h:268:29: warning: initialization of 'CROMol' {aka 'void *'} from 'Datum' {aka 'unsigned int'} makes pointer from integer without a cast [-Wint-conversion] 268 | #define PG_GETARG_DATUM(n) (fcinfo->args[n].value) | ^ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:502:18: note: in expansion of macro 'PG_GETARG_DATUM' 502 | CROMol mol = PG_GETARG_DATUM(1); | ^~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_smiles_transition': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:375:1: warning: control reaches end of non-void function [-Wreturn-type] 375 | } | ^ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mol_transition': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:510:1: warning: control reaches end of non-void function [-Wreturn-type] 510 | } | ^ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/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 -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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/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 -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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/rxn_op.c /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rxn_op.c:164:1: warning: multi-line comment [-Wcomment] 164 | // /* keep compiler quiet - no extra ; */ \ | ^ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rxn_op.c: In function 'reaction_to_svg': /build/reproducible-path/rdkit-202009.4/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 -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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/rdkit_gist.c /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c: In function 'soergeldistsign': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:239:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 239 | uint8 *as = (uint8 *)VARDATA(a); | ^~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c: In function 'soergeldist': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:274:16: warning: implicit declaration of function 'floor' [-Wimplicit-function-declaration] 274 | return (int) floor(10000*soergeldistsign(a, b)); | ^~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:274:16: warning: incompatible implicit declaration of built-in function 'floor' /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:41:1: note: include '' or provide a declaration of 'floor' 40 | #include "bitstring.h" +++ |+#include 41 | /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:261:10: warning: unused variable 'd' [-Wunused-variable] 261 | double d; | ^ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c: In function 'gmol_consistent': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:525:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 525 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:537:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 537 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:569:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 569 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c: In function 'rdkit_consistent': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:657:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 657 | int siglen = SIGLEN(query); | ^~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:672:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 672 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c: In function 'gsfp_consistent': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:707:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 707 | int sum, overlapSum, overlapN; | ^~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:713:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 713 | int nKey = (ISALLTRUE(key)) ? | ^~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c: In function 'greaction_consistent': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:786:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 786 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:803:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 803 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:831:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 831 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ At top level: /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:645:1: warning: 'rdkit_consistent' defined but not used [-Wunused-function] 645 | rdkit_consistent(GISTENTRY *entry, StrategyNumber strategy, bytea *key, bytea *query) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit_gist.c:260:1: warning: 'soergeldist' defined but not used [-Wunused-function] 260 | soergeldist(bytea *a, bytea *b) { | ^~~~~~~~~~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/bfp_gist.c /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/bfp_gist.c: In function 'merge_key': /build/reproducible-path/rdkit-202009.4/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 -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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/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 -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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/low_gist.c /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/low_gist.c: In function 'gslfp_consistent': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/low_gist.c:409:30: warning: implicit declaration of function 'searchSfpCache' [-Wimplicit-function-declaration] 409 | fcinfo->flinfo->fn_extra = searchSfpCache( | ^~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/low_gist.c:409:28: warning: assignment to 'void *' from 'int' makes pointer from integer without a cast [-Wint-conversion] 409 | fcinfo->flinfo->fn_extra = searchSfpCache( | ^ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/guc.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/cache.c /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/cache.c: In function 'createCache': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/cache.c:312:17: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 312 | methodsOrig = ctx->methods; | ^ In file included from /usr/include/postgresql/13/server/postgres.h:47, from /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/cache.c:33: /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/cache.c:341:19: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 341 | elog(ERROR, "Could not allocate %ld bytes", sizeof(*newholder)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~ | | | unsigned int /usr/include/postgresql/13/server/utils/elog.h:128:4: note: in definition of macro 'ereport_domain' 128 | __VA_ARGS__, errfinish(__FILE__, __LINE__, PG_FUNCNAME_MACRO); \ | ^~~~~~~~~~~ /usr/include/postgresql/13/server/utils/elog.h:215:2: note: in expansion of macro 'ereport' 215 | ereport(elevel, errmsg_internal(__VA_ARGS__)) | ^~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/cache.c:341:7: note: in expansion of macro 'elog' 341 | elog(ERROR, "Could not allocate %ld bytes", sizeof(*newholder)); | ^~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/cache.c:341:41: note: format string is defined here 341 | elog(ERROR, "Could not allocate %ld bytes", sizeof(*newholder)); | ~~^ | | | long int | %d g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -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-202009.4/Code -DRDKITVER='"007300"' -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/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-202009.4/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:24, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Conformer.h:14, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RDKitBase.h:25, from /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/adapter.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( | ^~~~~~~~~~~~~~~~~~~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/bitstring.c /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/bitstring.c: In function 'bitstringUnion': /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/bitstring.c:72:7: warning: unused variable 'i' [-Wunused-variable] 72 | int i; | ^ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/bitstring.c: In function 'bitstringIntersection': /build/reproducible-path/rdkit-202009.4/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 -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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -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-11/lib -Wl,--as-needed -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -L/build/reproducible-path/rdkit-202009.4/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-202009.4/Code/PgSQL/rdkit/rdkit.sql.in > rdkit--3.8.sql /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/rdkit_io.c /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/mol_op.c /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:375:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:395:12: warning: incompatible integer to pointer conversion initializing 'CROMol' (aka 'void *') with an expression of type 'Datum' (aka 'unsigned int') [-Wint-conversion] CROMol mol = PG_GETARG_DATUM(1); ^ ~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:423:12: warning: incompatible integer to pointer conversion initializing 'CROMol' (aka 'void *') with an expression of type 'Datum' (aka 'unsigned int') [-Wint-conversion] CROMol mol = PG_GETARG_DATUM(1); ^ ~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:491:12: warning: incompatible integer to pointer conversion initializing 'CROMol' (aka 'void *') with an expression of type 'Datum' (aka 'unsigned int') [-Wint-conversion] CROMol mol = PG_GETARG_DATUM(1); ^ ~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:502:12: warning: incompatible integer to pointer conversion initializing 'CROMol' (aka 'void *') with an expression of type 'Datum' (aka 'unsigned int') [-Wint-conversion] CROMol mol = PG_GETARG_DATUM(1); ^ ~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/mol_op.c:510:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 6 warnings generated. /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/bfp_op.c /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/sfp_op.c /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/rxn_op.c /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/rdkit_gist.c /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/bfp_gist.c /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/bfp_gin.c /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/low_gist.c /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/low_gist.c:409:30: warning: implicit declaration of function 'searchSfpCache' is invalid in C99 [-Wimplicit-function-declaration] fcinfo->flinfo->fn_extra = searchSfpCache( ^ /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/low_gist.c:409:28: warning: incompatible integer to pointer conversion assigning to 'void *' from 'int' [-Wint-conversion] fcinfo->flinfo->fn_extra = searchSfpCache( ^ ~~~~~~~~~~~~~~~ 2 warnings generated. /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/guc.c /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/cache.c /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/cache.c:312:17: warning: assigning to 'MemoryContextMethods *' (aka 'struct MemoryContextMethods *') from 'const MemoryContextMethods *' (aka 'const struct MemoryContextMethods *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] methodsOrig = ctx->methods; ^ ~~~~~~~~~~~~ 1 warning generated. /usr/bin/clang-11 -xc++ -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/adapter.cpp /usr/lib/llvm-11/bin/opt -module-summary -f adapter.bc -o adapter.bc /usr/bin/clang-11 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202009.4/Code -DRDKITVER='"007300"' -I. -I/build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit -I/usr/include/postgresql/13/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-202009.4/Code/PgSQL/rdkit/bitstring.c make[2]: Leaving directory '/build/reproducible-path/rdkit-202009.4/build-13' ### End 13 build ### (cd /build/reproducible-path/rdkit-202009.4/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 '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. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 1596 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 'MSCGEN_PATH' at line 1617 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: argument 'a4wide' for option PAPER_TYPE is not a valid enum value Using the default: a4! warning: doxygen no longer ships with the FreeSans font. You may want to clear or change DOT_FONTNAME. Otherwise you run the risk that the wrong font is being used for dot generated graphs. Doxygen version used: 1.9.1 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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directory /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Trajectory Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/Catalogs Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/DataStructs Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/Query Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/ML Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/ML/Cluster Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/ML/Cluster/Murtagh Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/ML/Data Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/DataManip Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/RDGeneral Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/hash Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/hash/detail Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/RDBoost Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/DistGeom Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/ForceField Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/Numerics Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/Numerics/EigenSolvers Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/Geometry Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/Features Searching for files in directory /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures Reading and parsing tag files Parsing files Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations/Abbreviations.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations/Abbreviations.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Atom.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Atom.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/atomic_data.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/atomic_data.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/AtomIterators.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/AtomIterators.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Bond.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Bond.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/BondIterators.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/BondIterators.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Canon.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Canon.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/CartesianProduct.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/CartesianProduct.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/Enumerate.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/Enumerate.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/RandomSample.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/RandomSample.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/PreprocessRxn.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/PreprocessRxn.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Reaction.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Reaction.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionFingerprints.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionFingerprints.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionParser.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionParser.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionPickler.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionPickler.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionRunner.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionRunner.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionUtils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionUtils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/SanitizeRxn.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/SanitizeRxn.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms/ChemTransforms.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms/ChemTransforms.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms/MolFragmenter.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms/MolFragmenter.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Chirality.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Chirality.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPLabeler.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPLabeler.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPMol.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPMol.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Configuration.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Configuration.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Sp2Bond.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Sp2Bond.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Descriptor.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Descriptor.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Digraph.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Digraph.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Edge.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Edge.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Mancude.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Mancude.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Node.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Node.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Priority.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Priority.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Pairlist.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Pairlist.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule1a.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule1a.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule1b.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule1b.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule2.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule2.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule3.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule3.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4a.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4a.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4b.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4b.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4c.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4c.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5New.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5New.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule6.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule6.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rules.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rules.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/SequenceRule.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/SequenceRule.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Sort.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Sort.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/TooManyNodesException.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/TooManyNodesException.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Conformer.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Conformer.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/DepictUtils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/DepictUtils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/EmbeddedFrag.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/EmbeddedFrag.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/RDDepictor.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/RDDepictor.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect/Deprotect.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect/Deprotect.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/AtomFeat.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/AtomFeat.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/AUTOCORR2D.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/AUTOCORR2D.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/AUTOCORR3D.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/AUTOCORR3D.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/BCUT.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/BCUT.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/CoulombMat.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/CoulombMat.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Crippen.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Crippen.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/EEM.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/EEM.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/GETAWAY.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/GETAWAY.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Lipinski.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Lipinski.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MolDescriptors.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MolDescriptors.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MolDescriptors3D.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MolDescriptors3D.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MolSurf.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MolSurf.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MORSE.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MORSE.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MQN.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MQN.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/PBF.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/PBF.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/PMI.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/PMI.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Property.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Property.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/RDF.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/RDF.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/RegisterDescriptor.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/RegisterDescriptor.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/USRDescriptor.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/USRDescriptor.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/WHIM.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/WHIM.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/details.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/details.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/Embedder.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/Embedder.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/FileParsers.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/FileParsers.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/FileParserUtils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/FileParserUtils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/GeneralFileReader.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/GeneralFileReader.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolFileStereochem.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolFileStereochem.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupParsing.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupParsing.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSupplier.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolWriters.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolWriters.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/PNGParser.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/PNGParser.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/ProximityBonds.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/ProximityBonds.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SequenceParsers.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SequenceParsers.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SequenceWriters.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SequenceWriters.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterCatalog.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterCatalog.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Filters.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Filters.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairs.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairs.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Fingerprints.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Fingerprints.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintUtil.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintUtil.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MACCS.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MACCS.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganFingerprints.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganFingerprints.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Composition2N.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Composition2N.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/DebugTrace.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/DebugTrace.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/FMCS.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/FMCS.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Graph.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Graph.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/MatchTable.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/MatchTable.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/RingMatchTableSet.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/RingMatchTableSet.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Seed.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Seed.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/SeedSet.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/SeedSet.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/SubstructMatchCustom.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/SubstructMatchCustom.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/SubstructureCache.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/SubstructureCache.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Target.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Target.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/TargetMatch.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/TargetMatch.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/FFConvenience.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/FFConvenience.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatGenerator.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatGenerator.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatParams.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatParams.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragFPGenerator.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragFPGenerator.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/GraphMol.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/GraphMol.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA/MMPA.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA/MMPA.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/AlignMolecules.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/AlignMolecules.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolBundle.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolBundle.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalog.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalog.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawText.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawText.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextCairo.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextCairo.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFT.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFT.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTCairo.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTCairo.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTJS.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTJS.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTQt.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTQt.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextJS.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextJS.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextQt.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextQt.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextSVG.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextSVG.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DJS.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DJS.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DQt.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DQt.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MultiMolDraw2D.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MultiMolDraw2D.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/mf.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/mf.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/MolHash.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/MolHash.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/nmmolhash.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/nmmolhash.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/details.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/details.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/MolInterchange.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/MolInterchange.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolOps.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolOps.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Charge.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Charge.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Fragment.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Fragment.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Metal.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Metal.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/MolStandardize.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/MolStandardize.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Normalize.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Normalize.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Tautomer.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Tautomer.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Validate.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Validate.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms/MolTransforms.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms/MolTransforms.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MonomerInfo.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MonomerInfo.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/new_canon.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/new_canon.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/GasteigerCharges.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/GasteigerCharges.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/GasteigerParams.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/GasteigerParams.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PeriodicTable.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PeriodicTable.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryAtom.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryAtom.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryBond.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryBond.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryOps.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryOps.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RDKitBase.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RDKitBase.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RDKitQueries.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RDKitQueries.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Resonance.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Resonance.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupCore.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupCore.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupData.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupData.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupMatch.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupMatch.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupScore.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupScore.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupUtils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupUtils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RingInfo.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RingInfo.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Rings.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Rings.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ROMol.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ROMol.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RWMol.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RWMol.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SanitException.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SanitException.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/detail.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/detail.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/SLNAttribs.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/SLNAttribs.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/SLNParse.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/SLNParse.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/SLNParseOps.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/SLNParseOps.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/primes.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/primes.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmartsWrite.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmartsWrite.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesParse.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesParse.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesParseOps.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesParseOps.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesWrite.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesWrite.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StereoGroup.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StereoGroup.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StructChecker/Pattern.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StructChecker/Pattern.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StructChecker/ReCharge.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StructChecker/ReCharge.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StructChecker/Stereo.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StructChecker/Stereo.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StructChecker/StripSmallFragments.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StructChecker/StripSmallFragments.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StructChecker/StructChecker.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StructChecker/StructChecker.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StructChecker/StructCheckerOptions.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StructChecker/StructCheckerOptions.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StructChecker/Tautomer.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StructChecker/Tautomer.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StructChecker/Utilites.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StructChecker/Utilites.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs/Subgraphs.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs/Subgraphs.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs/SubgraphUtils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs/SubgraphUtils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstanceGroup.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstanceGroup.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct/SubstructMatch.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct/SubstructMatch.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct/SubstructUtils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct/SubstructUtils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/PatternFactory.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/PatternFactory.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery/TautomerQuery.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery/TautomerQuery.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Trajectory/Snapshot.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Trajectory/Snapshot.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Trajectory/Trajectory.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Trajectory/Trajectory.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Catalogs/Catalog.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Catalogs/Catalog.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Catalogs/CatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Catalogs/CatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Catalogs/CatalogParams.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Catalogs/CatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DataStructs/base64.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DataStructs/base64.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DataStructs/BitOps.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DataStructs/BitOps.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DataStructs/BitVect.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DataStructs/BitVect.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DataStructs/BitVects.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DataStructs/BitVects.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DataStructs/BitVectUtils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DataStructs/BitVectUtils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DataStructs/DatastructsException.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DataStructs/DatastructsException.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DataStructs/DatastructsStreamOps.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DataStructs/DatastructsStreamOps.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DataStructs/DiscreteDistMat.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DataStructs/DiscreteDistMat.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DataStructs/DiscreteValueVect.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DataStructs/DiscreteValueVect.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DataStructs/ExplicitBitVect.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DataStructs/ExplicitBitVect.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DataStructs/FPBReader.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DataStructs/FPBReader.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DataStructs/MultiFPBReader.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DataStructs/MultiFPBReader.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DataStructs/SparseBitVect.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DataStructs/SparseBitVect.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DataStructs/SparseIntVect.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DataStructs/SparseIntVect.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Query/AndQuery.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Query/AndQuery.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Query/EqualityQuery.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Query/EqualityQuery.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Query/GreaterEqualQuery.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Query/GreaterEqualQuery.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Query/GreaterQuery.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Query/GreaterQuery.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Query/LessEqualQuery.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Query/LessEqualQuery.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Query/LessQuery.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Query/LessQuery.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Query/NullQueryAlgebra.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Query/NullQueryAlgebra.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Query/OrQuery.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Query/OrQuery.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Query/Query.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Query/Query.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Query/QueryObjects.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Query/QueryObjects.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Query/RangeQuery.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Query/RangeQuery.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Query/SetQuery.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Query/SetQuery.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Query/XOrQuery.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Query/XOrQuery.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/CorrMatGenerator.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/CorrMatGenerator.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/InfoBitRanker.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/InfoBitRanker.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/InfoGainFuncs.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/InfoGainFuncs.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/DistPicker.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/DistPicker.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/HierarchicalClusterPicker.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/HierarchicalClusterPicker.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/LeaderPicker.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/LeaderPicker.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/MaxMinPicker.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/MaxMinPicker.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/BadFileException.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/BadFileException.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/BoostEndInclude.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/BoostEndInclude.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/BoostStartInclude.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/BoostStartInclude.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/ConcurrentQueue.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/ConcurrentQueue.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/Dict.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/Dict.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/Exceptions.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/Exceptions.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/export.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/export.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/FileParseException.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/FileParseException.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/hanoiSort.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/hanoiSort.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/Invariant.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/Invariant.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/LocaleSwitcher.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/LocaleSwitcher.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/Ranking.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/Ranking.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDAny.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDAny.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDConfig.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDConfig.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDLog.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDLog.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDProps.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDProps.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDThreads.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDThreads.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDValue-doublemagic.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDValue-doublemagic.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDValue-taggedunion.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDValue-taggedunion.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDValue.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDValue.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/StreamOps.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/StreamOps.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/types.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/types.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/utils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/utils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/versions.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/versions.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDBoost/boost_numpy.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDBoost/boost_numpy.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDBoost/import_array.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDBoost/import_array.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDBoost/pyint_api.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDBoost/pyint_api.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDBoost/PySequenceHolder.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDBoost/PySequenceHolder.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DistGeom/BoundsMatrix.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DistGeom/BoundsMatrix.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DistGeom/ChiralSet.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DistGeom/ChiralSet.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DistGeom/ChiralViolationContrib.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DistGeom/ChiralViolationContrib.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DistGeom/DistGeomUtils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DistGeom/DistGeomUtils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DistGeom/DistViolationContrib.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DistGeom/DistViolationContrib.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DistGeom/FourthDimContrib.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DistGeom/FourthDimContrib.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/DistGeom/TriangleSmooth.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/DistGeom/TriangleSmooth.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/Contrib.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/Contrib.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/ForceField.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/ForceField.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/AngleBend.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/AngleBend.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/AngleConstraint.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/AngleConstraint.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/BondStretch.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/BondStretch.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/Contribs.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/Contribs.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/DistanceConstraint.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/DistanceConstraint.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/Nonbonded.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/Nonbonded.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/OopBend.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/OopBend.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/Params.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/Params.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/StretchBend.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/StretchBend.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/TorsionAngle.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/TorsionAngle.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/AngleBend.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/AngleBend.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/AngleConstraint.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/AngleConstraint.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/BondStretch.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/BondStretch.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/Contribs.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/Contribs.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/DistanceConstraint.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/DistanceConstraint.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/Inversion.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/Inversion.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/Nonbonded.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/Nonbonded.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/Params.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/Params.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/TorsionAngle.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/TorsionAngle.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/AlignPoints.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/AlignPoints.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Numerics/Conrec.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Numerics/Conrec.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Numerics/Matrix.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Numerics/Matrix.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer/BFGSOpt.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer/BFGSOpt.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Numerics/SquareMatrix.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Numerics/SquareMatrix.h... Preprocessing /build/reproducible-pat/build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h:61: warning: documented symbol 'for experimental torsion angle RDKit::DGeomHelpers::preferences' was not declared or defined. /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/nmmolhash.h:25: warning: documented symbol 'enum RDKIT_MOLHASH_EXPORT RDKit::MolHash::HashFunction' was not declared or defined. /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/nmmolhash.h:47: warning: documented symbol 'enum RDKIT_MOLHASH_EXPORT RDKit::MolHash::StripType' was not declared or defined. /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h:68: warning: documented symbol 'enum RDKIT_SCAFFOLDNETWORK_EXPORT RDKit::ScaffoldNetwork::EdgeType' was not declared or defined. /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:133: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:70: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:123: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:130: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryOps.h:515: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryOps.h:524: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:73: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:126: warning: Found unknown command '\override' h/rdkit-202009.4/Code/Numerics/SymmMatrix.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Numerics/SymmMatrix.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Numerics/Vector.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Numerics/Vector.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Geometry/Grid3D.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Geometry/Grid3D.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Geometry/GridUtils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Geometry/GridUtils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Geometry/Transform.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Geometry/Transform.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Geometry/Transform2D.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Geometry/Transform2D.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Geometry/Transform3D.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Geometry/Transform3D.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Geometry/UniformGrid3D.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Geometry/UniformGrid3D.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Geometry/Utils.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Geometry/Utils.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/Features/Feature.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/Features/Feature.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/ChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/ChemicalFeature.h... Preprocessing /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/FreeChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/FreeChemicalFeature.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Computing nesting relations for classes... Associating documentation with classes... 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 Abbreviations.h... Generating code for file AcidBaseCatalogEntry.h... Generating code for file AcidBaseCatalogParams.h... Generating code for file AcidBaseCatalogUtils.h... Generating code for file AlignMolecules.h... Generating code for file AlignPoints.h... Generating code for file AndQuery.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 Atom.h... Generating code for file AtomFeat.h... Generating code for file atomic_data.h... Generating code for file AtomIterators.h... Generating code for file AtomPairGenerator.h... Generating code for file AtomPairs.h... Generating code for file AtomTyper.h... Generating code for file AtomTyper.h... Generating code for file AUTOCORR2D.h... Generating code for file AUTOCORR3D.h... Generating code for file BadFileException.h... Generating code for file base64.h... Generating code for file BCUT.h... Generating code for file BFGSOpt.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 Bond.h... Generating code for file BondIterators.h... Generating code for file BondStretch.h... Generating code for file BondStretch.h... Generating code for file boost_numpy.h... Generating code for file BoostEndInclude.h... Generating code for file BoostStartInclude.h... Generating code for file BoundsMatrix.h... Generating code for file BoundsMatrixBuilder.h... Generating code for file Builder.h... Generating code for file Builder.h... Generating code for file Canon.h... Generating code for file CartesianProduct.h... Generating code for file Catalog.h... Generating code for file CatalogEntry.h... Generating code for file CatalogParams.h... Generating code for file Charge.h... Generating code for file ChemicalFeature.h... Generating code for file ChemTransforms.h... Generating code for file Chirality.h... Generating code for file ChiralSet.h... Generating code for file ChiralViolationContrib.h... Generating code for file CIPLabeler.h... Generating code for file CIPMol.h... Generating code for file Composition2N.h... Generating code for file ConcurrentQueue.h... Generating code for file Configuration.h... Generating code for file Conformer.h... Generating code for file ConnectivityDescriptors.h... Generating code for file Conrec.h... Generating code for file Contrib.h... Generating code for file Contribs.h... Generating code for file Contribs.h... Generating code for file CorrMatGenerator.h... Generating code for file CoulombMat.h... Generating code for file Crippen.h... Generating code for file Data3Ddescriptors.h... Generating code for file DatastructsException.h... Generating code for file DatastructsStreamOps.h... Generating code for file DebugTrace.h... Generating code for file DepictUtils.h... Generating code for file Deprotect.h... Generating code for file Descriptor.h... Generating code for file detail.h... Generating code for file details.h... Generating code for file details.h... Generating code for file Dict.h... Generating code for file Digraph.h... Generating code for file DiscreteDistMat.h... Generating code for file DiscreteValueVect.h... Generating code for file DistanceConstraint.h... Generating code for file DistanceConstraint.h... Generating code for file DistGeomUtils.h... Generating code for file DistPicker.h... Generating code for file DistViolationContrib.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 DrawTextFTQt.h... Generating code for file DrawTextFTSVG.h... Generating code for file DrawTextJS.h... Generating code for file DrawTextQt.h... Generating code for file DrawTextSVG.h... Generating code for file DuplicatedSeedCache.h... Generating code for file Edge.h... Generating code for file EEM.h... Generating code for file EmbeddedFrag.h... Generating code for file Embedder.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 EqualityQuery.h... Generating code for file EvenSamplePairs.h... Generating code for file Exceptions.h... Generating code for file ExplicitBitVect.h... Generating code for file export.h... Generating code for file Feature.h... Generating code for file FeatureParser.h... Generating code for file FFConvenience.h... Generating code for file FileParseException.h... Generating code for file FileParsers.h... Generating code for file FileParserUtils.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 FingerprintGenerator.h... Generating code for file Fingerprints.h... Generating code for file FingerprintUtil.h... Generating code for file FMCS.h... Generating code for file ForceField.h... Generating code for file FourthDimContrib.h... Generating code for file FPBReader.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 Fragment.h... Generating code for file FragmentCatalogEntry.h... Generating code for file FragmentCatalogParams.h... Generating code for file FragmentCatalogUtils.h... Generating code for file FreeChemicalFeature.h... Generating code for file FunctionalGroupHierarchy.h... Generating code for file GasteigerCharges.h... Generating code for file GasteigerParams.h... Generating code for file GeneralFileReader.h... Generating code for file GETAWAY.h... Generating code for file Graph.h... Generating code for file GraphMol.h... Generating code for file GreaterEqualQuery.h... Generating code for file GreaterQuery.h... Generating code for file Grid3D.h... Generating code for file GridUtils.h... Generating code for file hanoiSort.h... Generating code for file HierarchicalClusterPicker.h... Generating code for file import_array.h... Generating code for file InfoBitRanker.h... Generating code for file InfoGainFuncs.h... Generating code for file Invariant.h... Generating code for file Inversion.h... Generating code for file LeaderPicker.h... Generating code for file LessEqualQuery.h... Generating code for file LessQuery.h... Generating code for file Lipinski.h... Generating code for file LocaleSwitcher.h... Generating code for file MACCS.h... Generating code for file Mancude.h... Generating code for file MatchTable.h... Generating code for file Matrix.h... Generating code for file MaximumCommonSubgraph.h... Generating code for file MaxMinPicker.h... Generating code for file Metal.h... Generating code for file MetricFuncs.h... Generating code for file MetricMatrixCalc.h... Generating code for file mf.h... Generating code for file MHFP.h... Generating code for file MMFF.h... Generating code for file MMPA.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 MolChemicalFeature.h... Generating code for file MolChemicalFeatureDef.h... Generating code for file MolChemicalFeatureFactory.h... Generating code for file MolData3Ddescriptors.h... Generating code for file MolDescriptors.h... Generating code for file MolDescriptors3D.h... Generating code for file MolDraw2D.h... Generating code for file MolDraw2DCairo.h... Generating code for file MolDraw2DDetails.h... Generating code for file MolDraw2DJS.h... Generating code for file MolDraw2DQt.h... Generating code for file MolDraw2DSVG.h... Generating code for file MolDraw2DUtils.h... Generating code for file MolDraw2Dwx.h... Generating code for file MolEnumerator.h... Generating code for file MolFileStereochem.h... Generating code for file MolFragmenter.h... Generating code for file MolHash.h... Generating code for file MolInterchange.h... Generating code for file MolOps.h... Generating code for file MolPickler.h... Generating code for file MolSGroupParsing.h... Generating code for file MolSGroupWriting.h... Generating code for file MolStandardize.h... Generating code for file MolSupplier.h... Generating code for file MolSurf.h... Generating code for file MolTransforms.h... Generating code for file MolWriters.h... Generating code for file MonomerInfo.h... Generating code for file MorganFingerprints.h... Generating code for file MorganGenerator.h... Generating code for file MORSE.h... Generating code for file MQN.h... Generating code for file MultiFPBReader.h... Generating code for file MultiMolDraw2D.h... Generating code for file MultithreadedMolSupplier.h... Generating code for file MultithreadedSDMolSupplier.h... Generating code for file MultithreadedSmilesMolSupplier.h... Generating code for file new_canon.h... Generating code for file nmmolhash.h... Generating code for file Node.h... Generating code for file Nonbonded.h... Generating code for file Nonbonded.h... Generating code for file Normalize.h... Generating code for file NullQueryAlgebra.h... Generating code for file O3AAlignMolecules.h... Generating code for file OopBend.h... Generating code for file OrQuery.h... Generating code for file Pairlist.h... Generating code for file Params.h... Generating code for file Params.h... Generating code for file Pattern.h... Generating code for file PatternFactory.h... Generating code for file PBF.h... Generating code for file PeriodicTable.h... Generating code for file PMI.h... Generating code for file PNGParser.h... Generating code for file point.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... Generating code for file PowerEigenSolver.h... Generating code for file PreprocessRxn.h... Generating code for file primes.h... Generating code for file Priority.h... Generating code for file Property.h... Generating code for file ProximityBonds.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 Query.h... Generating code for file QueryAtom.h... Generating code for file QueryBond.h... Generating code for file QueryObjects.h... Generating code for file QueryOps.h... Generating code for file RandomSample.h... Generating code for file RandomSampleAllBBs.h... Generating code for file RangeQuery.h... Generating code for file Ranking.h... Generating code for file RDAny.h... Generating code for file RDConfig.h... Generating code for file RDDepictor.h... Generating code for file RDF.h... Generating code for file RDKitBase.h... Generating code for file RDKitFPGenerator.h... Generating code for file RDKitQueries.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 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 ReCharge.h... Generating code for file ReducedGraphs.h... Generating code for file RegisterDescriptor.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 RGroupMatch.h... Generating code for file RGroupScore.h... Generating code for file RGroupUtils.h... Generating code for file RingInfo.h... Generating code for file RingMatchTableSet.h... Generating code for file Rings.h... Generating code for file ROMol.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 RWMol.h... Generating code for file SanitException.h... Generating code for file SanitizeRxn.h... Generating code for file ScaffoldNetwork.h... Generating code for file Seed.h... Generating code for file SeedSet.h... Generating code for file SequenceParsers.h... Generating code for file SequenceRule.h... Generating code for file SequenceWriters.h... Generating code for file SetQuery.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 SmartsWrite.h... Generating code for file SmilesParse.h... Generating code for file SmilesParseOps.h... Generating code for file SmilesWrite.h... Generating code for file Snapshot.h... Generating code for file Sort.h... Generating code for file Sp2Bond.h... Generating code for file SparseBitVect.h... Generating code for file SparseIntVect.h... Generating code for file SquareMatrix.h... Generating code for file Stereo.h... Generating code for file StereoGroup.h... Generating code for file StreamOps.h... Generating code for file StretchBend.h... Generating code for file StripSmallFragments.h... Generating code for file StructChecker.h... Generating code for file StructCheckerOptions.h... Generating code for file Subgraphs.h... Generating code for file SubgraphUtils.h... Generating code for file SubstanceGroup.h... Generating code for file SubstructLibrary.h... Generating code for file SubstructLibrarySerialization.h... Generating code for file SubstructMatch.h... Generating code for file SubstructMatchCustom.h... Generating code for file SubstructureCache.h... Generating code for file SubstructUtils.h... Generating code for file SymmMatrix.h... Generating code for file Target.h... Generating code for file TargetMatch.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 TautomerQuery.h... Generating code for file Tetrahedral.h... Generating code for file TooManyNodesException.h... Generating code for file TopologicalTorsionGenerator.h... Generating code for file TorsionAngle.h... Generating code for file TorsionAngle.h... Generating code for file TorsionAngleM6.h... Generating code for file TorsionConstraint.h... Generating code for file TorsionConstraint.h... Generating code for file TorsionPreferences.h... Generating code for file Trajectory.h... Generating code for file Transform.h... Generating code for file Transform2D.h... Generating code for file Transform3D.h... Generating code for file TransformCatalogEntry.h... Generating code for file TransformCatalogParams.h... Generating code for file TransformCatalogUtils.h... Generating code for file TriangleSmooth.h... Generating code for file types.h... Generating code for file UFF.h... Generating code for file UniformGrid3D.h... Generating code for file USRDescriptor.h... Generating code for file Utilites.h... Generating code for file Utils.h... Generating code for file utils.h... Generating code for file Validate.h... Generating code for file Vector.h... Generating code for file versions.h... Generating code for file WHIM.h... Generating code for file XOrQuery.h... Generating file documentation... Generating docs for file Abbreviations.h... Generating docs for file AcidBaseCatalogEntry.h... Generating docs for file AcidBaseCatalogParams.h... Generating docs for file AcidBaseCatalogUtils.h... Generating docs for file AlignMolecules/build/reproducible-path/rdkit-202009.4/Code/DataStructs/BitOps.h:184: warning: found at different nesting level (7) than expected (4) /build/reproducible-path/rdkit-202009.4/Code/DataStructs/BitOps.h:185: warning: end of comment block while expecting command .h... Generating docs for file AlignPoints.h... Generating docs for file AndQuery.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 Atom.h... Generating docs for file AtomFeat.h... Generating docs for file atomic_data.h... Generating docs for file AtomIterators.h... Generating docs for file AtomPairGenerator.h... Generating docs for file AtomPairs.h... Generating docs for file AtomTyper.h... Generating docs for file AtomTyper.h... Generating docs for file AUTOCORR2D.h... Generating docs for file AUTOCORR3D.h... Generating docs for file BadFileException.h... Generating docs for file base64.h... Generating docs for file BCUT.h... Generating docs for file BFGSOpt.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 Bond.h... Generating docs for file BondIterators.h... Generating docs for file BondStretch.h... Generating docs for file BondStretch.h... Generating docs for file boost_numpy.h... Generating docs for file BoostEndInclude.h... Generating docs for file BoostStartInclude.h... Generating docs for file BoundsMatrix.h... Generating docs for file BoundsMatrixBuilder.h... Generating docs for file Builder.h... Generating docs for file Builder.h... Generating docs for file Canon.h... Generating docs for file CartesianProduct.h... Generating docs for file Catalog.h... Generating docs for file CatalogEntry.h... Generating docs for file CatalogParams.h... Generating docs for file Charge.h... Generating docs for file ChemicalFeature.h... Generating docs for file ChemTransforms.h... Generating docs for file Chirality.h... Generating docs for file ChiralSet.h... Generating docs for file ChiralViolationContrib.h... Generating docs for file CIPLabeler.h... Generating docs for file CIPMol.h... Generating docs for file Composition2N.h... Generating docs for file ConcurrentQueue.h... Generating docs for file Configuration.h... Generating docs for file Conformer.h... Generating docs for file ConnectivityDescriptors.h... Generating docs for file Conrec.h... Generating docs for file Contrib.h... Generating docs for file Contribs.h... Generating docs for file Contribs.h... Generating docs for file CorrMatGenerator.h... Generating docs for file CoulombMat.h... Generating docs for file Crippen.h... Generating docs for file Data3Ddescriptors.h... Generating docs for file DatastructsException.h... Generating docs for file DatastructsStreamOps.h... Generating docs for file DebugTrace.h... Generating docs for file DepictUtils.h... Generating docs for file Deprotect.h... Generating docs for file Descriptor.h... Generating docs for file detail.h... Generating docs for file details.h... Generating docs for file details.h... Generating docs for file Dict.h... Generating docs for file Digraph.h... Generating docs for file DiscreteDistMat.h... Generating docs for file DiscreteValueVect.h... Generating docs for file DistanceConstraint.h... Generating docs for file DistanceConstraint.h... Generating docs for file DistGeomUtils.h... Generating docs for file DistPicker.h... Generating docs for file DistViolationContrib.h... Generating docs for file DrawText.h... Generating docs for file DrawTextCairo.h... Generating docs for file DrawTextFT.h... Generating docs for file DrawTextFTCairo.h... Generating docs for file DrawTextFTJS.h... Generating docs for file DrawTextFTQt.h... Generating docs for file DrawTextFTSVG.h... Generating docs for file DrawTextJS.h... Generating docs for file DrawTextQt.h... Generating docs for file DrawTextSVG.h... Generating docs for file DuplicatedSeedCache.h... Generating docs for file Edge.h... Generating docs for file EEM.h... Generating docs for file EmbeddedFrag.h... Generating docs for file Embedder.h... Generating docs for file Enumerate.h... Generating docs for file EnumerateBase.h... Generating docs for file EnumerateTypes.h... Generating docs for file EnumerationPickler.h... Generating docs for file EnumerationStrategyBase.h... Generating docs for file EqualityQuery.h... Generating docs for file EvenSamplePairs.h... Generating docs for file Exceptions.h... Generating docs for file ExplicitBitVect.h... Generating docs for file export.h... Generating docs for file Feature.h... Generating docs for file FeatureParser.h... Generating docs for file FFConvenience.h... Generating docs for file FileParseException.h... Generating docs for file FileParsers.h... Generating docs for file FileParserUtils.h... Generating docs for file FilterCatalog.h... Generating docs for file FilterCatalogEntry.h... Generating docs for file FilterMatcherBase.h... Generating docs for file FilterMatchers.h... Generating docs for file Filters.h... Generating docs for file FingerprintGenerator.h... Generating docs for file Fingerprints.h... Generating docs for file FingerprintUtil.h... Generating docs for file FMCS.h... Generating docs for file ForceField.h... Generating docs for file FourthDimContrib.h... Generating docs for file FPBReader.h... Generating docs for file FragCatalogEntry.h... Generating docs for file FragCatalogUtils.h... Generating docs for file FragCatGenerator.h... Generating docs for file FragCatParams.h... Generating docs for file FragFPGenerator.h... Generating docs for file Fragment.h... Generating docs for file FragmentCatalogEntry.h... Generating docs for file FragmentCatalogParams.h... Generating docs for file FragmentCatalogUtils.h... Generating docs for file FreeChemicalFeature.h... Generating docs for file FunctionalGroupHierarchy.h... Generating docs for file GasteigerCharges.h... Generating docs for file GasteigerParams.h... Generating docs for file GeneralFileReader.h... Generating docs for file GETAWAY.h... Generating docs for file Graph.h... Generating docs for file GraphMol.h... Generating docs for file GreaterEqualQuery.h... Generating docs for file GreaterQuery.h... Generating docs for file Grid3D.h... Generating docs for file GridUtils.h... Generating docs for file hanoiSort.h... Generating docs for file HierarchicalClusterPicker.h... Generating docs for file import_array.h... Generating docs for file InfoBitRanker.h... Generating docs for file InfoGainFuncs.h... Generating docs for file Invariant.h... Generating docs for file Inversion.h... Generating docs for file LeaderPicker.h... Generating docs for file LessEqualQuery.h... Generating docs for file LessQuery.h... Generating docs for file Lipinski.h... Generating docs for file LocaleSwitcher.h... Generating docs for file MACCS.h... Generating docs for file Mancude.h... Generating docs for file MatchTable.h... Generating docs for file Matrix.h... Generating docs for file MaximumCommonSubgraph.h... Generating docs for file MaxMinPicker.h... Generating docs for file Metal.h... Generating docs for file MetricFuncs.h... Generating docs for file MetricMatrixCalc.h... Generating docs for file mf.h... Generating docs for file MHFP.h... Generating docs for file MMFF.h... Generating docs for file MMPA.h... Generating docs for file MolBundle.h... Generating docs for file MolCatalog.h... Generating docs for file MolCatalogEntry.h... Generating docs for file MolCatalogParams.h... Generating docs for file MolChemicalFeature.h... Generating docs for file MolChemicalFeatureDef.h... Generating docs for file MolChemicalFeatureFactory.h... Generating docs for file MolData3Ddescriptors.h... Generating docs for file MolDescriptors.h... Generating docs for file MolDescriptors3D.h... Generating docs for file MolDraw2D.h... Generating docs for file MolDraw2DCairo.h... Generating docs for file MolDraw2DDetails.h... Generating docs for file MolDraw2DJS.h... Generating docs for file MolDraw2DQt.h... Generating docs for file MolDraw2DSVG.h... Generating docs for file MolDraw2DUtils.h... Generating docs for file MolDraw2Dwx.h... Generating docs for file MolEnumerator.h... Generating docs for file MolFileStereochem.h... Generating docs for file MolFragmenter.h... Generating docs for file MolHash.h... Generating docs for file/build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryOps.h:515: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryOps.h:524: warning: Found unknown command '\overloadquery' MolInterchange.h... Generating docs for file MolOps.h... Generating docs for file MolPickler.h... Generating docs for file MolSGroupParsing.h... Generating docs for file MolSGroupWriting.h... Generating docs for file MolStandardize.h... Generating docs for file MolSupplier.h... Generating docs for file MolSurf.h... Generating docs for file MolTransforms.h... Generating docs for file MolWriters.h... Generating docs for file MonomerInfo.h... Generating docs for file MorganFingerprints.h... Generating docs for file MorganGenerator.h... Generating docs for file MORSE.h... Generating docs for file MQN.h... Generating docs for file MultiFPBReader.h... Generating docs for file MultiMolDraw2D.h... Generating docs for file MultithreadedMolSupplier.h... Generating docs for file MultithreadedSDMolSupplier.h... Generating docs for file MultithreadedSmilesMolSupplier.h... Generating docs for file new_canon.h... Generating docs for file nmmolhash.h... Generating docs for file Node.h... Generating docs for file Nonbonded.h... Generating docs for file Nonbonded.h... Generating docs for file Normalize.h... Generating docs for file NullQueryAlgebra.h... Generating docs for file O3AAlignMolecules.h... Generating docs for file OopBend.h... Generating docs for file OrQuery.h... Generating docs for file Pairlist.h... Generating docs for file Params.h... Generating docs for file Params.h... Generating docs for file Pattern.h... Generating docs for file PatternFactory.h... Generating docs for file PBF.h... Generating docs for file PeriodicTable.h... Generating docs for file PMI.h... Generating docs for file PNGParser.h... Generating docs for file point.h... Generating docs for file PositionConstraint.h... Generating docs for file PositionConstraint.h... Generating docs for file PowerEigenSolver.h... Generating docs for file PreprocessRxn.h... Generating docs for file primes.h... Generating docs for file Priority.h... Generating docs for file Property.h... Generating docs for file ProximityBonds.h... Generating docs for file pyint_api.h... Generating docs for file PySequenceHolder.h... Generating docs for file python.h... Generating docs for file python_streambuf.h... Generating docs for file Query.h... Generating docs for file QueryAtom.h... Generating docs for file QueryBond.h... Generating docs for file QueryObjects.h... Generating docs for file QueryOps.h... Generating docs for file RandomSample.h... Generating docs for file RandomSampleAllBBs.h... Generating docs for file RangeQuery.h... Generating docs for file Ranking.h... Generating docs for file RDAny.h... Generating docs for file RDConfig.h... Generating docs for file RDDepictor.h... Generating docs for file RDF.h... Generating docs for file RDKitBase.h... Generating docs for file RDKitFPGenerator.h... Generating docs for file RDKitQueries.h... Generating docs for file RDLog.h... Generating docs for file RDProps.h... 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 Reaction.h... Generating docs for file ReactionFingerprints.h... Generating docs for file ReactionParser.h... Generating docs for file ReactionPickler.h... Generating docs for file ReactionRunner.h... Generating docs for file ReactionUtils.h... Generating docs for file ReCharge.h... Generating docs for file ReducedGraphs.h... Generating docs for file RegisterDescriptor.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 RGroupMatch.h... Generating docs for file RGroupScore.h... Generating docs for file RGroupUtils.h... Generating docs for file RingInfo.h... Generating docs for file RingMatchTableSet.h... Generating docs for file Rings.h... Generating docs for file ROMol.h... Generating docs for file Rule1a.h... Generating docs for file Rule1b.h... Generating docs for file Rule2.h... Generating docs for file Rule3.h... Generating docs for file Rule4a.h... Generating docs for file Rule4b.h... Generating docs for file Rule4c.h... Generating docs for file Rule5.h... Generating docs for file Rule5New.h... Generating docs for file Rule6.h... Generating docs for file Rules.h... Generating docs for file RWMol.h... Generating docs for file SanitException.h... Generating docs for file SanitizeRxn.h... Generating docs for file ScaffoldNetwork.h... Generating docs for file Seed.h... Generating docs for file SeedSet.h... Generating docs for file SequenceParsers.h... Generating docs for file SequenceRule.h... Generating docs for file SequenceWriters.h... Generating docs for file SetQuery.h... Generating docs for file ShapeEncoder.h... Generating docs for file ShapeUtils.h... Generating docs for file SLNAttribs.h... Generating docs for file SLNParse.h... Generating docs for file SLNParseOps.h... Generating docs for file SmartsWrite.h... Generating docs for file SmilesParse.h... Generating docs for file SmilesParseOps.h... Generating docs for file SmilesWrite.h... Generating docs for file Snapshot.h... Generating docs for file Sort.h... Generating docs for file Sp2Bond.h... Generating docs for file SparseBitVect.h... Generating docs for file SparseIntVect.h... Generating docs for file SquareMatrix.h... Generating docs for file Stereo.h... Generating docs for file StereoGroup.h... Generating docs for file StreamOps.h... Generating docs for file StretchBend.h... Generating docs for file StripSmallFragments.h... Generating docs for file StructChecker.h... Generating docs for file StructCheckerOptions.h... Generating docs for file Subgraphs.h... Generating docs for file SubgraphUtils.h... Generating docs for file SubstanceGroup.h... Generating docs for file SubstructLibrary.h... Generating docs for file SubstructLibrarySerialization.h... Generating docs for file SubstructMatch.h... Generating docs for file SubstructMatchCustom.h... Generating docs for file SubstructureCache.h... Generating docs for file SubstructUtils.h... Generating docs for file SymmMatrix.h... Generating docs for file Target.h... Generating docs for file TargetMatch.h... Generating docs for file Tautomer.h... Generating docs for file Tautomer.h... Generating docs for file TautomerCatalogEntry.h... Generating docs for file TautomerCatalogParams.h... Generating docs for file TautomerCatalogUtils.h... Generating docs for file TautomerQuery.h... Generating docs for file Tetrahedral.h... Generating docs for file TooManyNodesException.h... Generating docs for file TopologicalTorsionGenerator.h... Generating docs for file TorsionAngle.h... Generating docs for file TorsionAngle.h... Generating docs for file TorsionAngleM6.h... Generating docs for file TorsionConstraint.h... Generating docs for file TorsionConstraint.h... Generating docs for file TorsionPreferences.h... Generating docs for file Trajectory.h... Generating docs for file Transform.h... Generating docs for file Transform2D.h... Generating docs for file Transform3D.h... Generating docs for file TransformCatalogEntry.h... Generating docs for file TransformCatalogParams.h... Generating docs for file TransformCatalogUtils.h... Generating docs for file TriangleSmooth.h... Generating docs for file types.h... Generating docs for file UFF.h... Generating docs for file UniformGrid3D.h... Generating docs for file USRDescriptor.h... Generating docs for file Utilites.h... Generating docs for file Utils.h... Generating docs for file utils.h... Generating docs for file Validate.h... Generating docs for file Vector.h... Generating docs for file versions.h... Generating docs for file WHIM.h... Generating docs for file XOrQuery.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... Genera/build/reproducible-path/rdkit-202009.4/Code/DistGeom/DistGeomUtils.h:118: 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-202009.4/Code/ForceField/ForceField.h:162: 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-202009.4/Code/ForceField/ForceField.h:162: 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-202009.4/Code/ForceField/ForceField.h:156: 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-202009.4/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-202009.4/Code/ForceField/MMFF/AngleBend.h:40: 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-202009.4/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-202009.4/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-202009.4/Code/ForceField/MMFF/AngleConstraint.h:37: 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-202009.4/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-202009.4/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-202009.4/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-202009.4/Code/ForceField/MMFF/BondStretch.h:36: 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-202009.4/Code/ForceField/MMFF/Nonbonded.h:35: 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-202009.4/Code/ForceField/MMFF/Nonbonded.h:59: 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' ting docs for compound KeyErrorException... Generating docs for compound MolData3Ddescriptors... Generating docs for compound PySequenceHolder... Generating docs for compound SparseBitVect... Generating docs for compound ValueErrorException... Generating namespace index... Generating docs for namespace BFGSOpt Generating docs for namespace boost Generating docs for namespace boost::logging Generating docs for compound boost::logging::rdLogger... Generating docs for namespace boost_adaptbx Generating docs for namespace boost_adaptbx::python Generating docs for compound boost_adaptbx::python::streambuf... Generating docs for nested compound boost_adaptbx::python::streambuf::istream... Generating docs for nested compound boost_adaptbx::python::streambuf::ostream... Generating docs for compound boost_adaptbx::python::streambuf_capsule... Generating docs for compound boost_adaptbx::python::ostream... Generating docs for namespace ChemicalFeatures Generating docs for compound ChemicalFeatures::ChemicalFeature... Generating docs for compound ChemicalFeatures::FreeChemicalFeature... Generating docs for namespace conrec Generating docs for compound conrec::ConrecSegment... Generating docs for namespace DistGeom Generating docs for compound DistGeom::BoundsMatrix... Generating docs for compound DistGeom::ChiralSet... Generating docs for compound DistGeom::ChiralViolationContrib... Generating docs for compound DistGeom::DistViolationContrib... Generating docs for compound DistGeom::FourthDimContrib... Generating docs for namespace ForceFields Generating docs for compound ForceFields::ForceFieldContrib... Generating docs for compound ForceFields::ForceField... Generating docs for namespace ForceFields::CrystalFF Generating docs for compound ForceFields::CrystalFF::TorsionAngleContribM6... Generating docs for compound ForceFields::CrystalFF::CrystalFFDetails... Generating docs for namespace ForceFields::MMFF Generating docs for compound ForceFields::MMFF::AngleBendContrib... 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::VdWContrib... Generating docs for compound ForceFields::MMFF::EleContrib... Generating docs for compound ForceFields::MMFF::OopBendContrib... Generating docs for compound ForceFields::MMFF::MMFFDef... Generating docs for compound ForceFields::MMFF::MMFFProp... Generating docs for compound ForceFields::MMFF::MMFFPBCI... Generating docs for compound ForceFields::MMFF::MMFFChg... Generating docs for compound ForceFields::MMFF::MMFFBond... Generating docs for compound ForceFields::MMFF::MMFFHerschbachLaurie... Generating docs for compound ForceFields::MMFF::MMFFCovRadPauEle... Generating docs for compound ForceFields::MMFF::MMFFAngle... Generating docs for compound ForceFields::MMFF::MMFFStbn... Generating docs for compound ForceFields::MMFF::MMFFOop... Generating docs for compound ForceFields::MMFF::MMFFTor... Generating docs for compound ForceFields::MMFF::MMFFVdW... Generating docs for compound ForceFields::MMFF::MMFFVdWRijstarEps... Generating docs for compound ForceFields::MMFF::MMFFAromCollection... Generating docs for compound ForceFields::MMFF::MMFFDefCollection... Generating docs for compound ForceFields::MMFF::MMFFPropCollection... Generating docs for compound ForceFields::MMFF::MMFFPBCICollection... Generating docs for compound ForceFields::MMFF::MMFFChgCollection... Generating docs for compound ForceFields::MMFF::MMFFBondCollection... Generating docs for compound ForceFields::MMFF::MMFFBndkCollection... Generating docs for compound ForceFields::MMFF::MMFFHerschbachLaurieCollection... Generating docs for compound ForceFields::MMFF::MMFFCovRadPauEleCollection... Generating docs for compound ForceFields::MMFF::MMFFAngleCollection... Generating docs for compound ForceFields::MMFF::MMFFStbnCollection... Generating docs for compound ForceFields::MMFF::MMFFDfsbCollection... Generating docs for comp/build/reproducible-path/rdkit-202009.4/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-202009.4/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-202009.4/Code/ForceField/MMFF/StretchBend.h:41: 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-202009.4/Code/ForceField/MMFF/TorsionAngle.h:35: 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-202009.4/Code/ForceField/MMFF/TorsionAngle.h:46: 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-202009.4/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-202009.4/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-202009.4/Code/ForceField/UFF/AngleConstraint.h:37: 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-202009.4/Code/ForceField/UFF/Inversion.h:39: 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-202009.4/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-202009.4/Code/GraphMol/Depictor/RDDepictor.h:72: warning: The following parameter of RDDepict::compute2DCoords(RDKit::ROMol &mol, const RDGeom::INT_POINT2D_MAP *coordMap=nullptr, bool canonOrient=false, bool clearConfs=true, unsigned int nFlipsPerSample=0, unsigned int nSamples=0, int sampleSeed=0, bool permuteDeg4Nodes=false, bool forceRDKit=false) is not documented: parameter 'forceRDKit' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/RDDepictor.h:127: warning: The following parameter of RDDepict::compute2DCoordsMimicDistMat(RDKit::ROMol &mol, const DOUBLE_SMART_PTR *dmat=nullptr, bool canonOrient=true, bool clearConfs=true, double weightDistMat=0.5, unsigned int nFlipsPerSample=3, unsigned int nSamples=100, int sampleSeed=25, bool permuteDeg4Nodes=true, bool forceRDKit=false) is not documented: parameter 'forceRDKit' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/RDDepictor.h:159: warning: The following parameter of RDDepict::generateDepictionMatching2DStructure(RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=static_cast< RDKit::ROMol * >(nullptr), bool acceptFailure=false, bool forceRDKit=false) is not documented: parameter 'forceRDKit' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/RDDepictor.h:167: 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-202009.4/Code/GraphMol/Depictor/RDDepictor.h:186: warning: The following parameters of RDDepict::generateDepictionMatching3DStructure(RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=nullptr, bool acceptFailure=false, bool forceRDKit=false) are not documented: parameter 'referencePattern' parameter 'forceRDKit' ound ForceFields::MMFF::MMFFOopCollection... Generating docs for compound ForceFields::MMFF::MMFFTorCollection... Generating docs for compound ForceFields::MMFF::MMFFVdWCollection... 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 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::BondStretchContrib... Generating docs for compound ForceFields::UFF::DistanceConstraintContrib... Generating docs for compound ForceFields::UFF::InversionContrib... Generating docs for compound ForceFields::UFF::vdWContrib... Generating docs for compound ForceFields::UFF::UFFBond... Generating docs for compound ForceFields::UFF::UFFAngle... Generating docs for compound ForceFields::UFF::UFFTor... Generating docs for compound ForceFields::UFF::UFFInv... Generating docs for compound ForceFields::UFF::UFFVdW... Generating docs for compound ForceFields::UFF::AtomicParams... 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 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::LessEqualQuery... Generating docs for compound Queries::LessQuery... Generating docs for compound Queries::OrQuery... Generating docs for compound Queries::Int2Type... 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 compound Rankers::pairGreater... Generating docs for compound Rankers::pairLess... Generating docs for compound Rankers::argless... Generating docs for namespace RDCatalog Generating docs for compound RDCatalog::Catalog... Generating docs for compound RDCatalog::HierarchCatalog... Generating docs for nested compound RDCatalog::HierarchCatalog::vertex_entry_t... Generating docs for compound RDCatalog::CatalogEntry... Generating docs for compound RDCatalog::CatalogParams... Generating docs for namespace RDDataManip Generating docs for compound RDDataManip::MetricMatrixCalc... Generating docs for namespace RDDepict Generating docs for compound RDDepict::gtIIPair... Generating docs for compound RDDepict::EmbeddedAtom... Generating docs for compound RDDepict::EmbeddedFrag... Generating docs for compound RDDepict::DepictException... 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::GridException... Generating docs for compound RDGeom::Grid3D... Generating docs for compound RDGeom::Point... Generating docs for compound RDGeom::Point3D... Generating docs for compound RDGeom::Point2D... 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 nam/build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryOps.h:515: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryOps.h:524: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstanceGroup.h:231: warning: The following parameter of RDKit::addSubstanceGroup(ROMol &mol, SubstanceGroup sgroup) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202009.4/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-202009.4/Code/GraphMol/FileParsers/SequenceParsers.h:110: warning: The following parameter of RDKit::HELMToMol(const char *helm, bool sanitize=true) is not documented: parameter 'helm' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Fingerprints.h:105: 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-202009.4/Code/GraphMol/QueryOps.h:515: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryOps.h:524: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/FileParsers.h:60: warning: argument 'line' from the argument list of RDKit::MolDataStreamToMol has multiple @param documentation sections /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesWrite.h:152: warning: argument 'doRandom' of command @param is not found in the argument list of RDKit::MolFragmentToCXSmiles(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-202009.4/Code/GraphMol/SmilesParse/SmilesWrite.h:99: 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-202009.4/Code/GraphMol/SmilesParse/SmilesWrite.h:145: 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-202009.4/Code/GraphMol/FileParsers/FileParsers.h:318: 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-202009.4/Code/GraphMol/FileParsers/FileParsers.h:329: 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-202009.4/Code/GraphMol/SmilesParse/SmilesWrite.h:74: 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-202009.4/Code/GraphMol/Fingerprints/Fingerprints.h:144: 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-202009.4/Code/GraphMol/Fingerprints/Fingerprints.h:26: 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-202009.4/Code/GraphMol/Fingerprints/Fingerprints.h:53: 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-202009.4/Code/GraphMol/ChemReactions/ReactionRunner.h:97: warning: The following parameter of RDKit::reduceProductToSideChains(const ROMOL_SPTR &product, bool addDummyAtoms=true) is not documented: parameter 'product' /build/reproducible-path/rdkit-202009.4/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-202009.4/Code/GraphMol/ChemReactions/ReactionRunner.h:64: 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-202009.4/Code/GraphMol/ChemReactions/ReactionRunner.h:77: 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-202009.4/Code/GraphMol/Substruct/SubstructMatch.h:56: 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-202009.4/Code/GraphMol/Substruct/SubstructMatch.h:63: 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-202009.4/Code/GraphMol/Substruct/SubstructMatch.h:69: 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-202009.4/Code/GraphMol/Substruct/SubstructMatch.h:76: 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-202009.4/Code/GraphMol/Substruct/SubstructMatch.h:145: 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-202009.4/Code/GraphMol/ChemReactions/Reaction.h:207: 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-202009.4/Code/GraphMol/ChemReactions/Reaction.h:219: 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-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:99: 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-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:105: 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-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:322: 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 99 in file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:322: 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-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:415: 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 99 in file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:415: warning: The following parameter of RDKit::ExclusionList::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintGenerator.h:109: warning: The following parameter 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=0 is not documented: parameter 'AdditionalOutput' espace RDInfoTheory Generating docs for compound RDInfoTheory::BitCorrMatGenerator... Generating docs for compound RDInfoTheory::InfoBitRanker... Generating docs for namespace RDKit Generating docs for compound RDKit::Atom... Generating docs for compound RDKit::atomicData... Generating docs for compound RDKit::AtomIterator_... Generating docs for compound RDKit::HeteroatomIterator_... Generating docs for compound RDKit::AromaticAtomIterator_... Generating docs for compound RDKit::QueryAtomIterator_... Generating docs for compound RDKit::MatchingAtomIterator_... Generating docs for compound RDKit::Bond... Generating docs for compound RDKit::BondIterator_... Generating docs for compound RDKit::ConstBondIterator_... Generating docs for compound RDKit::CartesianProductStrategy... Generating docs for compound RDKit::EnumerationParams... Generating docs for compound RDKit::EnumerateLibrary... Generating docs for compound RDKit::EnumerateLibraryBase... Generating docs for compound RDKit::EnumerationStrategyException... Generating docs for compound RDKit::EnumerationStrategyBase... Generating docs for compound RDKit::EvenSamplePairsStrategy... Generating docs for compound RDKit::RandomSampleStrategy... Generating docs for compound RDKit::RandomSampleAllBBsStrategy... Generating docs for compound RDKit::ChemicalReactionException... Generating docs for compound RDKit::ChemicalReaction... Generating docs for compound RDKit::ReactionFingerprintParams... Generating docs for compound RDKit::ChemicalReactionParserException... Generating docs for compound RDKit::ReactionPicklerException... Generating docs for compound RDKit::ReactionPickler... Generating docs for compound RDKit::RxnSanitizeException... Generating docs for compound RDKit::ConformerException... Generating docs for compound RDKit::Conformer... Generating docs for compound RDKit::MolFileUnhandledFeatureException... Generating docs for compound RDKit::MolSupplier... Generating docs for compound RDKit::ForwardSDMolSupplier... Generating docs for compound RDKit::SDMolSupplier... Generating docs for compound RDKit::SmilesMolSupplier... Generating docs for compound RDKit::TDTMolSupplier... Generating docs for compound RDKit::PDBMolSupplier... Generating docs for compound RDKit::MolWriter... Generating docs for compound RDKit::SmilesWriter... Generating docs for compound RDKit::SDWriter... Generating docs for compound RDKit::TDTWriter... Generating docs for compound RDKit::PDBWriter... Generating docs for compound RDKit::FilterCatalogParams... Generating docs for compound RDKit::FilterCatalog... Generating docs for compound RDKit::FilterCatalogEntry... Generating docs for compound RDKit::FilterMatch... Generating docs for compound RDKit::FilterMatcherBase... Generating docs for compound RDKit::SmartsMatcher... Generating docs for compound RDKit::ExclusionList... Generating docs for compound RDKit::FilterHierarchyMatcher... Generating docs for compound RDKit::FilterData_t... Generating docs for compound RDKit::FilterProperty_t... Generating docs for compound RDKit::AdditionalOutput... Generating docs for compound RDKit::FingerprintArguments... Generating docs for compound RDKit::AtomEnvironment... Generating docs for compound RDKit::AtomEnvironmentGenerator... Generating docs for compound RDKit::AtomInvariantsGenerator... Generating docs for compound RDKit::BondInvariantsGenerator... Generating docs for compound RDKit::FingerprintGenerator... Generating docs for compound RDKit::UnimplementedFPException... Generating docs for compound RDKit::MCSAtomCompareParameters... Generating docs for compound RDKit::MCSBondCompareParameters... Generating docs for compound RDKit::MCSProgressData... Generating docs for compound RDKit::MCSParameters... Generating docs for compound RDKit::MCSResult... 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::MolBundle... Generating docs for compound RDK/build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:334: warning: argument 'highlight_atoms' from the argument list of RDKit::MolDraw2D::drawMolecule has multiple @param documentation sections /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:334: 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-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:387: 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-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:387: 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-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:387: 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-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:411: warning: argument 'highlight_atoms' from the argument list of RDKit::MolDraw2D::drawMolecules has multiple @param documentation sections /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:411: 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' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:377: warning: The following parameter of RDKit::MolDraw2D::drawMoleculeWithHighlights(const ROMol &mol, const std::string &legend, 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_linewidth_multipliers' /build/reproducible-path/rdkit-202009.4/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) it::FixedMolSizeMolBundle... Generating docs for compound RDKit::MolCatalogEntry... Generating docs for compound RDKit::MolCatalogParams... Generating docs for compound RDKit::FeatureFileParseException... Generating docs for compound RDKit::MolChemicalFeature... Generating docs for compound RDKit::MolChemicalFeatureDef... Generating docs for compound RDKit::MolChemicalFeatureFactory... Generating docs for compound RDKit::DrawText... Generating docs for compound RDKit::DrawTextCairo... Generating docs for compound RDKit::DrawTextFT... Generating docs for compound RDKit::DrawTextFTCairo... Generating docs for compound RDKit::DrawTextFTJS... Generating docs for compound RDKit::DrawTextFTQt... Generating docs for compound RDKit::DrawTextFTSVG... Generating docs for compound RDKit::DrawTextJS... Generating docs for compound RDKit::DrawTextQt... Generating docs for compound RDKit::DrawTextSVG... Generating docs for compound RDKit::DrawColour... Generating docs for compound RDKit::StringRect... Generating docs for compound RDKit::MolDrawOptions... 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::MultiMolDraw2D... Generating docs for compound RDKit::MolPicklerException... Generating docs for compound RDKit::MolPickler... Generating docs for compound RDKit::AtomMonomerInfo... Generating docs for compound RDKit::AtomPDBResidueInfo... Generating docs for compound RDKit::GasteigerParams... Generating docs for compound RDKit::PeriodicTable... Generating docs for compound RDKit::QueryAtom... Generating docs for compound RDKit::QueryBond... Generating docs for compound RDKit::AtomRingQuery... Generating docs for compound RDKit::RecursiveStructureQuery... Generating docs for compound RDKit::HasPropQuery... Generating docs for compound RDKit::HasPropWithValueQuery... Generating docs for compound RDKit::HasPropWithValueQuery< TargetPtr, std::string >... Generating docs for compound RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect >... Generating docs for compound RDKit::ResonanceMolSupplierCallback... Generating docs for compound RDKit::ResonanceMolSupplier... Generating docs for compound RDKit::RCore... Generating docs for compound RDKit::RGroupData... Generating docs for compound RDKit::RGroupDecompositionParameters... Generating docs for compound RDKit::RGroupDecomposition... Generating docs for compound RDKit::RGroupDecompData... Generating docs for nested compound RDKit::RGroupDecompData::UsedLabels... Generating docs for compound RDKit::RGroupMatch... Generating docs for compound RDKit::CartesianProduct... Generating docs for compound RDKit::RingInfo... 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::ROMol... Generating docs for compound RDKit::RWMol... Generating docs for compound RDKit::MolSanitizeException... Generating docs for compound RDKit::AtomSanitizeException... Generating docs for compound RDKit::AtomValenceException... Generating docs for compound RDKit::AtomKekulizeException... Generating docs for compound RDKit::KekulizeException... Generating docs for compound RDKit::SLNParseException... Generating docs for compound RDKit::SmilesParserParams... Generating docs for compound RDKit::SmilesParseException... Generating docs for compound RDKit::StereoGroup... Generating docs for compound RDKit::SubstanceGroupException... 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::SubstructMatchParameters... Genera/build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations/Abbreviations.h:105: 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-202009.4/Code/GraphMol/Fingerprints/AtomPairGenerator.h:103: warning: The following parameter 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 is not documented: parameter 'AdditionalOutput' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairs.h:121: 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-202009.4/Code/GraphMol/Fingerprints/FingerprintUtil.h:77: 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-202009.4/Code/GraphMol/Canon.h:114: 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-202009.4/Code/GraphMol/Chirality.h:106: warning: The following parameter of RDKit::Chirality::findPotentialStereo(ROMol &mol, bool cleanIt, bool flagPossible=true) is not documented: parameter 'flagPossible' ting docs for compound RDKit::MolHolderBase... Generating docs for compound RDKit::MolHolder... Generating docs for compound RDKit::CachedMolHolder... Generating docs for compound RDKit::CachedSmilesMolHolder... Generating docs for compound RDKit::CachedTrustedSmilesMolHolder... Generating docs for compound RDKit::FPHolderBase... Generating docs for compound RDKit::PatternHolder... Generating docs for compound RDKit::SubstructLibrary... Generating docs for compound RDKit::TautomerQuery... Generating docs for compound RDKit::Snapshot... Generating docs for compound RDKit::Trajectory... Generating docs for compound RDKit::DataStructsExplicitBitVecPropHandler... Generating docs for compound RDKit::DiscreteDistMat... Generating docs for compound RDKit::DiscreteValueVect... Generating docs for compound RDKit::FPBReader... Generating docs for compound RDKit::MultiFPBReader... Generating docs for compound RDKit::SparseIntVect... Generating docs for compound RDKit::BadFileException... Generating docs for compound RDKit::Dict... Generating docs for nested compound RDKit::Dict::Pair... Generating docs for compound RDKit::FileParseException... Generating docs for compound RDKit::RDAny... Generating docs for compound RDKit::RDProps... Generating docs for compound RDKit::RDValue... Generating docs for compound RDKit::CustomPropHandler... Generating docs for compound RDKit::ltDouble... Generating docs for compound RDKit::larger_of... Generating docs for compound RDKit::charptr_functor... 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::AtomPairAtomInvGenerator... Generating docs for compound RDKit::AtomPair::AtomPairArguments... Generating docs for compound RDKit::AtomPair::AtomPairAtomEnv... 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::MolStackUnion... Generating docs for compound RDKit::Canon::MolStackElem... Generating docs for compound RDKit::Canon::bondholder... Generating docs for compound RDKit::Canon::canon_atom... Generating docs for compound RDKit::Canon::SpecialChiralityAtomCompareFunctor... Generating docs for compound RDKit::Canon::SpecialSymmetryAtomCompareFunctor... Generating docs for compound RDKit::Canon::AtomCompareFunctor... Generating docs for compound RDKit::Canon::ChiralAtomCompareFunctor... Generating docs for namespace RDKit::Chirality Generating docs for compound RDKit::Chirality::StereoInfo... Generating docs for namespace RDKit::CIPLabeler Generating docs for compound RDKit::CIPLabeler::CIPMolSpan... Generating docs for nested compound RDKit::CIPLabeler::CIPMolSpan::CIPMolIter... Generating docs for compound RDKit::CIPLabeler::CIPMol... Generating docs for compound RDKit::CIPLabeler::Configuration... Generating docs for compound RDKit::CIPLabeler::Sp2Bond... Generating docs for compound RDKit::CIPLabeler::Tetrahedral... 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::Priority... Generating docs for compound RDKit::CIPLabeler::PairList... 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 RD/build/reproducible-path/rdkit-202009.4/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-202009.4/Code/GraphMol/Descriptors/Lipinski.h:52: warning: The following parameter of RDKit::Descriptors::calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default) is not documented: parameter 'useStrictDefinition' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/USRDescriptor.h:81: 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-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:86: 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 99 in file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:86: 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-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:148: 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 99 in file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:148: warning: The following parameter of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:204: 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 99 in file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.h:204: 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-202009.4/Code/GraphMol/Fingerprints/MHFP.h:104: warning: found tag without matching /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.h:116: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::CreateShingling(const ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=true, unsigned char min_radius=1) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.h:144: warning: found tag without matching /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.h:156: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::Encode(ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=true, unsigned char min_radius=1) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.h:202: warning: found tag without matching /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.h:216: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::EncodeSECFP(ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=true, unsigned char min_radius=1, size_t length=2048) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA/MMPA.h:36: 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;!$(*=,#[!#6])]!@!=!#[*]") is not documented: parameter 'pattern' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA/MMPA.h:57: warning: The following parameter of RDKit::MMPA::fragmentMol(const ROMol &mol, std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR >> &result, unsigned int minCuts, unsigned int maxCuts, unsigned int maxCutBonds, const std::string &pattern="[#6+0;!$(*=,#[!#6])]!@!=!#[*]") is not documented: parameter 'pattern' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/AlignMolecules.h:136: warning: argument 'probeId' of command @param is not found in the argument list of RDKit::MolAlign::CalcRMS(ROMol &probeMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, const RDNumeric::DoubleVector *weights=nullptr) /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/AlignMolecules.h:136: warning: argument 'refId' of command @param is not found in the argument list of RDKit::MolAlign::CalcRMS(ROMol &probeMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, const RDNumeric::DoubleVector *weights=nullptr) /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/AlignMolecules.h:155: warning: The following parameters of RDKit::MolAlign::CalcRMS(ROMol &probeMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, const RDNumeric::DoubleVector *weights=nullptr) are not documented: parameter 'prbCid' parameter 'refCid' Kit::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::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::CrippenParams... Generating docs for compound RDKit::Descriptors::CrippenParamCollection... Generating docs for compound RDKit::Descriptors::PropertyFunctor... Generating docs for compound RDKit::Descriptors::Properties... 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::Or... Generating docs for compound RDKit::FilterMatchOps::Not... Generating docs for namespace RDKit::FMCS Generating docs for compound RDKit::FMCS::Composition2N... Generating docs for compound RDKit::FMCS::ExecStatistics... Generating docs for compound RDKit::FMCS::DuplicatedSeedCache... Generating docs for nested compound RDKit::FMCS::DuplicatedSeedCache::TKey... Generating docs for compound RDKit::FMCS::Graph... Generating docs for compound RDKit::FMCS::TArray2D... Generating docs for compound RDKit::FMCS::MaximumCommonSubgraph... Generating docs for compound RDKit::FMCS::RingMatchTableSet... Generating docs for compound RDKit::FMCS::MolFragment... Generating docs for compound RDKit::FMCS::NewBond... 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 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::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::MolAlignException... Generating docs for compound RDKit::MolAlign::O3AFuncData... Generating docs for compound RDKit::MolAlign::O3AConstraint... Generating docs for compound RDKit::MolAlign::O3AConstraintVect... Generating docs for compound RDKit::MolAlign::MolHistogram... Generating docs for compound RDKit::MolAlign::LAP... Generating docs for compound RDKit::MolAlign::SDM... Generating docs for compound RDKit::MolAlign::O3A... Generating docs for /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:70: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:73: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:70: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:73: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:123: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:126: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:130: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:133: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:133: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:123: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:130: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.h:126: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolOps.h:749: 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-202009.4/Code/GraphMol/MolOps.h:302: warning: The following parameter of RDKit::MolOps::mergeQueryHs(const ROMol &mol, bool mergeUnmappedOnly=false) is not documented: parameter 'mergeUnmappedOnly' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h:191: warning: argument 'OutputType' of command @param is not found in the argument list of RDKit::MorganFingerprint::getMorganGenerator(const unsigned int radius, const bool countSimulation=false, const bool includeChirality=false, const bool useBondTypes=true, const bool onlyNonzeroInvariants=false, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, BondInvariantsGenerator *bondInvariantsGenerator=nullptr, const std::uint32_t fpSize=2048, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const bool ownsAtomInvGen=false, const bool ownsBondInvGen=false) /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h:191: warning: argument 'radiu' of command @param is not found in the argument list of RDKit::MorganFingerprint::getMorganGenerator(const unsigned int radius, const bool countSimulation=false, const bool includeChirality=false, const bool useBondTypes=true, const bool onlyNonzeroInvariants=false, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, BondInvariantsGenerator *bondInvariantsGenerator=nullptr, const std::uint32_t fpSize=2048, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const bool ownsAtomInvGen=false, const bool ownsBondInvGen=false) /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h:228: warning: argument 'countSimulation' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h:228: warning: argument 'includeChirality' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h:228: warning: argument 'onlyNonzeroInvariants' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h:228: warning: The following parameter of RDKit::MorganFingerprint::getMorganGenerator(const unsigned int radius, const bool countSimulation=false, const bool includeChirality=false, const bool useBondTypes=true, const bool onlyNonzeroInvariants=false, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, BondInvariantsGenerator *bondInvariantsGenerator=nullptr, const std::uint32_t fpSize=2048, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const bool ownsAtomInvGen=false, const bool ownsBondInvGen=false) is not documented: parameter 'radius' namespace RDKit::MolDraw2D_detail 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::MolEnumeratorOp... Generating docs for compound RDKit::MolEnumerator::PositionVariationOp... Generating docs for compound RDKit::MolEnumerator::LinkNodeOp... Generating docs for compound RDKit::MolEnumerator::MolEnumeratorParams... 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 namespace RDKit::MolOps Generating docs for compound RDKit::MolOps::RemoveHsParameters... Generating docs for compound RDKit::MolOps::AdjustQueryParameters... 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::ChargeCorrection... Generating docs for compound RDKit::MolStandardize::Reionizer... Generating docs for compound RDKit::MolStandardize::Uncharger... Generating docs for compound RDKit::MolStandardize::FragmentRemover... Generating docs for compound RDKit::MolStandardize::LargestFragmentChooser... Generating docs for nested compound RDKit::MolStandardize::LargestFragmentChooser::Largest... Generating docs for compound RDKit::MolStandardize::FragmentCatalogEntry... Generating docs for compound RDKit::MolStandardize::FragmentCatalogParams... Generating docs for compound RDKit::MolStandardize::MetalDisconnector... Generating docs for compound RDKit::MolStandardize::CleanupParameters... Generating docs for compound RDKit::MolStandardize::Normalizer... Generating docs for compound RDKit::MolStandardize::Tautomer... Generating docs for compound RDKit::MolStandardize::TautomerEnumeratorResult... Generating docs for nested compound RDKit::MolStandardize::TautomerEnumeratorResult::const_iterator... Generating docs for compound RDKit::MolStandardize::TautomerEnumeratorCallback... Generating docs for compound RDKit::MolStandardize::TautomerEnumerator... Generating docs for compound RDKit::MolStandardize::TautomerCatalogEntry... Generating docs for compound RDKit::MolStandardize::TautomerCatalogParams... 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::ValidationErrorInfo... Generating docs for compound RDKit::MolStandardize::ValidationMethod... Generating docs for compound RDKit::MolStandardize::RDKitValidation... Generating docs for compound RDKit::MolStandardize::MolVSValidations... Generating docs for compound RDKit::MolStandardize::NoAtomValidation... Generating docs for compound RDKit::MolStandardize::FragmentValidation... Generating docs for compound RDKit::MolStandardize::NeutralValidation... Generating docs for compound RDKit::MolStandardize::IsotopeValidation... Generating docs for compound RDKit::MolStandardize::MolVSValidation... Generating docs for compound RDKit::MolStandardize::AllowedAtomsValidation... Generating docs for compound RDKit::MolStandardize::DisallowedAtomsValidation... Generating docs for namespace RDKit::MolStandardize::TautomerScoringFunctions Generating docs for namespace RDKit::MorganFingerprint Generating docs for compound RDKit::MorganFingerprint::MorganAtomInvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganFeatureAtomInvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganBondInvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganArguments... Generating docs f/build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.h:151: warning: The following parameter 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 is not documented: parameter 'AdditionalOutput' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganFingerprints.h:157: 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-202009.4/Code/GraphMol/Fingerprints/RDKitFPGenerator.h:76: warning: The following parameter 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 is not documented: parameter 'AdditionalOutput' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs/ReducedGraphs.h:34: 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-202009.4/Code/GraphMol/ChemReactions/SanitizeRxn.h:126: 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-202009.4/Code/GraphMol/ChemReactions/SanitizeRxn.h:156: 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-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:89: 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-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:109: 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-202009.4/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-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:44: 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-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:57: warning: The following parameter 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 is not documented: parameter 'AdditionalOutput' /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/HierarchicalClusterPicker.h:80: 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-202009.4/Code/SimDivPickers/LeaderPicker.h:47: 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-202009.4/Code/SimDivPickers/LeaderPicker.h:47: 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-202009.4/Code/SimDivPickers/LeaderPicker.h:97: 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-202009.4/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-202009.4/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 or compound RDKit::MorganFingerprint::MorganAtomEnv... Generating docs for compound RDKit::MorganFingerprint::MorganEnvGenerator... 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::RDKitFPAtomInvGenerator... Generating docs for compound RDKit::RDKitFP::RDKitFPAtomEnv... Generating docs for compound RDKit::RDKitFP::RDKitFPEnvGenerator... 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::ScaffoldNetworkParams... Generating docs for compound RDKit::ScaffoldNetwork::NetworkEdge... Generating docs for compound RDKit::ScaffoldNetwork::ScaffoldNetwork... 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::ChargeFix... Generating docs for compound RDKit::StructureCheck::Ligand... Generating docs for compound RDKit::StructureCheck::AugmentedAtom... Generating docs for compound RDKit::StructureCheck::IncEntry... Generating docs for compound RDKit::StructureCheck::PathEntry... Generating docs for compound RDKit::StructureCheck::StructCheckerOptions... Generating docs for compound RDKit::StructureCheck::StructChecker... Generating docs for compound RDKit::StructureCheck::StructCheckTautomer... Generating docs for compound RDKit::StructureCheck::Neighbourhood... 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::BlockLogs... 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 graph info page... Generating directory documentation... Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member 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 17650/65536 hits=133798 misses=20433 finished... (cd /build/reproducible-path/rdkit-202009.4/Docs/Book; RDBASE=/build/reproducible-path/rdkit-202009.4 /usr/bin/make html) make[2]: Entering directory '/build/reproducible-path/rdkit-202009.4/Docs/Book' mkdir -p _build/html/cppapi cp -r /build/reproducible-path/rdkit-202009.4/Code/docs/* _build/html/cppapi cp -r C++Examples _build/html/ sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v3.4.3 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 309 source files that are out of date updating environment: [new config] 309 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... [ 0%] Cartridge reading sources... [ 0%] GettingStartedInC++ reading sources... 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[100%] source/rdkit.utils.spiral /build/reproducible-path/rdkit-202009.4/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' WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' 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' 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' 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.DSViewer' 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' 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.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' 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' 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' 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' 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' 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' 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' 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' 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.LazyGenerator' 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' 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.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' 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' 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' 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.Subshape.testCombined' 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' 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' 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.rdChemReactions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202009.4/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.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-202009.4/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-202009.4/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-202009.4/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.rdMolHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202009.4/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-202009.4/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-202009.4/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' WARNING: autodoc: failed to import module 'Chem.rdStructChecker' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202009.4/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.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' WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised: No module named 'rdkit' 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' 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.HierarchyVis' 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' 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' WARNING: autodoc: failed to import module 'DistanceGeometry.DistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202009.4/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' 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' 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' 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' 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' 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' 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.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' 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.DecTree.randomtest' 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' 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' 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-202009.4/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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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.NodeLib.demo' 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' 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.chemdraw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemdraw_qax' 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.comhack' 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-202009.4/Docs/Book/data/README.md: WARNING: document isn't included in any toctree /build/reproducible-path/rdkit-202009.4/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... 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The HTML pages are in _build/html. make[2]: Leaving directory '/build/reproducible-path/rdkit-202009.4/Docs/Book' (cd /build/reproducible-path/rdkit-202009.4/Docs/Book; RDBASE=/build/reproducible-path/rdkit-202009.4 /usr/bin/make latexpdf) make[2]: Entering directory '/build/reproducible-path/rdkit-202009.4/Docs/Book' mkdir -p _build/html/cppapi cp -r /build/reproducible-path/rdkit-202009.4/Code/docs/* _build/html/cppapi sphinx-build -b latex -d _build/doctrees . _build/latex Running Sphinx v3.4.3 making output directory... done WARNING: html_static_path entry '_static' does not exist loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 0 added, 298 changed, 0 removed reading sources... [ 0%] index reading sources... [ 0%] source/rdkit reading sources... [ 1%] source/rdkit.Avalon reading sources... [ 1%] source/rdkit.Avalon.pyAvalonTools reading sources... 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[100%] source/rdkit.utils.spiral /build/reproducible-path/rdkit-202009.4/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' WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' 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' 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' 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.DSViewer' 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' 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.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' 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' 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' 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' 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' 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' 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' 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' 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.LazyGenerator' 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' 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.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' 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' 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' 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.Subshape.testCombined' 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' 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' 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.rdChemReactions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202009.4/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.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-202009.4/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-202009.4/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-202009.4/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.rdMolHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202009.4/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-202009.4/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-202009.4/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' WARNING: autodoc: failed to import module 'Chem.rdStructChecker' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202009.4/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.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' WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised: No module named 'rdkit' 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' 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.HierarchyVis' 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' 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' WARNING: autodoc: failed to import module 'DistanceGeometry.DistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202009.4/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' 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' 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' 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' 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' 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' 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.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' 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.DecTree.randomtest' 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' 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' 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-202009.4/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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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' 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.NodeLib.demo' 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' 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.chemdraw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemdraw_qax' 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.comhack' 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-202009.4/Docs/Book/data/README.md: WARNING: document isn't included in any toctree /build/reproducible-path/rdkit-202009.4/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.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.LazyGenerator 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.Subshape.testCombined 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.DSViewer 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.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.rdStructChecker 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.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.HierarchyVis 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.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.DecTree.randomtest 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.NodeLib.demo 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.chemdraw source/rdkit.utils.chemdraw_qax source/rdkit.utils.chemutils source/rdkit.utils.comhack 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-202009.4/Docs/Book/GettingStartedInC++.md:145: WARNING: None:any reference target not found: ./C++Examples/example1.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:167: WARNING: None:any reference target not found: ./C++Examples/example1.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:181: WARNING: None:any reference target not found: ./C++Examples/example1.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:194: WARNING: None:any reference target not found: ./C++Examples/example1.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:209: WARNING: None:any reference target not found: ./C++Examples/example2.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:233: WARNING: None:any reference target not found: ./C++Examples/example2.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:253: WARNING: None:any reference target not found: ./C++Examples/example2.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:270: WARNING: None:any reference target not found: ./C++Examples/example2.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:294: WARNING: None:any reference target not found: ./C++Examples/example2.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:308: WARNING: None:any reference target not found: ./C++Examples/example3.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:321: WARNING: None:any reference target not found: ./C++Examples/example3.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:330: WARNING: None:any reference target not found: ./C++Examples/example3.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:349: WARNING: None:any reference target not found: ./C++Examples/example3.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:370: WARNING: None:any reference target not found: ./C++Examples/example3.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:397: WARNING: None:any reference target not found: ./C++Examples/example3.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:433: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:462: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:495: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:506: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:519: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:530: WARNING: None:any reference target not found: ./C++Examples/example4.cpp /build/reproducible-path/rdkit-202009.4/Docs/Book/GettingStartedInC++.md:543: WARNING: 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Running LaTeX files through pdflatex... make -C _build/latex all-pdf make[3]: Entering directory '/build/reproducible-path/rdkit-202009.4/Docs/Book/_build/latex' latexmk -pdf -dvi- -ps- 'RDKit.tex' Rc files read: /etc/LatexMk ./latexmkrc Latexmk: This is Latexmk, John Collins, 29 September 2020, version: 4.70b. Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -recorder "RDKit.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Underfull \hbox (badness 10000) in paragraph at lines 123--124 []\T1/ptm/m/n/10 Cheminformatics 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 217. [2] [3] [4] Chapter 2. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [5] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [7] [8] [9] [10] Underfull \hbox (badness 10000) in paragraph at lines 746--747 []\T1/ptm/m/n/10 You can en-able sup-port for the Avalon toolkit by adding the ar-gu-ment [11] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 815. (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) Underfull \hbox (badness 10000) in paragraph at lines 844--845 []\T1/ptm/m/n/10 Add \T1/pcr/m/n/10 #define BOOST_PYTHON_NO_PY_SIGNATURES \T1/p tm/m/n/10 at the top of \T1/pcr/m/n/10 Code/GraphMol/Wrap/ [12] [13] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 951. Underfull \hbox (badness 10000) in paragraph at lines 951--952 \T1/pcr/m/n/10 installed to \T1/ptm/m/n/10 C:\boost\T1/pcr/m/n/10 , and that yo u will build the RDKit from a directory named Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 969. [14] Underfull \hbox (badness 10000) in paragraph at lines 991--992 []\T1/ptm/m/n/10 Run cmake. Here's an ex-am-ple ba-sic com-mand line for 64bit win-dows that will Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/ptm/m/n/10 down-load the InChI and Avalon toolkit sources from the InChI Tr ust and Source-Forge Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/ptm/m/n/10 repos-i-to-ries, re-spec-tively, and build the Post-greSQL car-t ridge for the in-stalled ver-sion Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/ptm/m/n/10 of Post-greSQL:\T1/pcr/m/n/10 cmake -DRDK_BUILD_PYTHON_WRAPPERS= ON -DBOOST_ROOT=C:/ Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/pcr/m/n/10 boost -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/pcr/m/n/10 -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\Postgre SQL\9.5" Underfull \hbox (badness 10000) in paragraph at lines 1000--1001 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" Underfull \hbox (badness 10000) in paragraph at lines 1006--1007 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" [15] [16] Chapter 3. [17] Underfull \hbox (badness 10000) in paragraph at lines 1102--1103 []\T1/ptm/m/n/10 displays a mes-sage like: \T1/pcr/m/n/10 [12:18:01] Explicit v alence for atom # 1 O greater than [18] [19] [20] LaTeX Warning: Hyper reference `GettingStartedInPython:chem-vs-allchem' on page 21 undefined on input line 1303. [21] Overfull \vbox (1.28346pt too high) detected at line 1420 [22] [23] LaTeX Warning: Hyper reference `GettingStartedInPython:the-sssr-problem' on pag e 24 undefined on input line 1518. [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1652--1654 []\T1/ptm/m/n/10 Another op-tion for Com-pute2DCoords al-lows you to gen-er-ate 2D de-pic-tions for molecules that Underfull \hbox (badness 7649) in paragraph at lines 1652--1654 \T1/ptm/m/n/10 closely mimic 3D con-for-ma-tions. This is avail-able us-ing the func-tion \T1/pcr/m/n/10 rdkit.Chem.AllChem. 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[60 <./similarity_map_crippen.png>] [61] Overfull \hbox (59.44438pt too wide) in paragraph at lines 3309--3309 []\T1/pcr/m/n/9 [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- [62 <./reaction1.png>] [63 <./reaction1_highlight.png>] [64] [65] [66] [67] LaTeX Warning: Hyper reference `RDKit_Book::doc' on page 68 undefined on input line 3679. [68] [69] [70] Underfull \hbox (badness 6792) in paragraph at lines 3922--3925 []\T1/ptm/m/n/10 Or we can use the bit rank-ing func-tion-al-ity from the \T1/p cr/m/n/10 rdkit.ML.InfoTheory.rdInfoTheory. [71] [72] [73] [74 <./picture_6.png>] [75] Overfull \hbox (520.56647pt too wide) in alignment at lines 4359--4509 [] [] [] Overfull \hbox (520.56647pt too wide) in alignment at lines 4509--4518 [] [] [] [76] Package longtable Warning: Column widths have changed (longtable) in table 1 on input line 4518. 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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] Overfull \vbox (5.17178pt too high) detected at line 5258 [87] [88] [89] Underfull \hbox (badness 10000) in paragraph at lines 5644--5646 []\T1/ptm/m/n/10 metals, [90] [91 <./parastereo_2.png> <./parastereo_1.png>] [92 <./potential_stereo_dou ble_bond1.png> <./potential_stereo_double_bond2.png> <./potential_stereo_double _bond3.png>] [93] [94] [95] [96] [97] [98] [99] LaTeX Warning: Hyper reference `RDKit_Book:ph4-figure' on page 100 undefined on input line 6353. 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[107] Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/phv/m/n/10 Mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- [108] [109 <./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 7558) in paragraph at lines 7102--7104 []\T1/ptm/m/n/10 It is pos-si-ble to enu-mer-ate the el-e-ments of a \T1/pcr/m/ n/10 StereoGroup \T1/ptm/m/n/10 us-ing the func-tion \T1/pcr/m/n/10 rdkit.Chem. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Underfull \hbox (badness 10000) in paragraph at lines 7116--7117 []\T1/ptm/m/n/10 Reactions also pre-serve \T1/pcr/m/n/10 StereoGroup\TS1/cmtt/m /n/10 ``\T1/pcr/m/n/10 s. Product atoms are included in the Underfull \hbox (badness 10000) in paragraph at lines 7159--7161 [] Underfull \hbox (badness 10000) in paragraph at lines 7270--7272 [] [110] [111 <./EnhancedStereoSSS_molA.png> <./EnhancedStereoSSS_molB.png> <./Enh ancedStereoSSS_molC.png> <./EnhancedStereoSSS_molD.png> <./EnhancedStereoSSS_mo lE.png> <./EnhancedStereoSSS_molF.png> <./EnhancedStereoSSS_molG.png>] [112] [113] [114] Chapter 5. 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@H[]\T1/pcr/m/n/9 ][]2[]CCC N2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC[S[]+[]](C)[O[]- [119] Overfull \hbox (1096.24321pt too wide) in paragraph at lines 7778--7778 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][ ]2[]CCCN2C([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O) [C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]([C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)CC)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CO)NC([]=[]O)[C[]\T1/pcr /b/n/9 @H[]\T1/pcr/m/n/9 ](C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]([C []\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)O)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T 1/pcr/m/n/9 ][]2[]CSSC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](NC1[]=[]O)C([]=[]O) N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1cnc[nH][]1[])C([]=[]O)N[C[]\T1/p cr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1 /pcr/m/n/9 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lines 7782--7782 []\T1/pcr/m/n/9 CCCCCCCCCCCCCCCCNC([]=[]O)CN(CC([]=[]O)NC(C)(C)C([]=[]O)N[C[]@[ ][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC([]=[]N)N )C([]=[]O)N1CCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[]O)N[C[]@[][]\T1 /pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC([]=[]N)N)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(N)[]=[]O)C(N)[]=[]O)C([]=[]O)c1cccnc1| Overfull \hbox (383.44402pt too wide) in paragraph at lines 7783--7783 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2cc ccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]@[][] \T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/p cr/m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C(C)C)NC([ ]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCSC)NC1[]=[]O| Overfull \hbox (394.244pt too wide) in paragraph at lines 7784--7784 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2cc ccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]@[][] \T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/p cr/m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C(C)C)NC([ ]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC[S[]+[]](C)[O[]- Overfull \hbox (448.24394pt too wide) in paragraph at lines 7785--7785 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2c[ nH]c3ccccc23)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccccc2)NC([]=[] O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]@[][]\T1/pcr/b/ n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ] (CCSC)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]\T1/ pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC[S[]+[]](C)[O[]- Overfull \hbox (270.04414pt too wide) in paragraph at lines 7786--7786 [][]\T1/pcr/m/n/9 ])NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C(C)C)NC([] =[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2c[nH]c3ccccc23)NC([]=[]O)[C[]\T1/ pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr /m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCC N2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC[S[]+[]](C)[O[]- Overfull \hbox (550.84383pt too wide) in paragraph at lines 7787--7787 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]\T1/pcr/b/n/9 @H[ ]\T1/pcr/m/n/9 ](N)C([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C([]=[]O)N[C []@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)C([]=[]O)N[C[]\T1/pcr/b/n/9 @H[ ]\T1/pcr/m/n/9 ](C([]=[]O)N1CCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[ ]O)N1CCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[]O)N[C[]\T1/pcr/b/n/9 @ H[]\T1/pcr/m/n/9 ](CCC([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCC([ ]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)C([]=[]O)O)Cc1ccccc1)C c1ccccc1)C(C)C)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)CC| [120] [121] [122] Overfull \vbox (1.18257pt too high) detected at line 7995 [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] Chapter 6. [133] Underfull \hbox (badness 10000) in paragraph at lines 8641--8644 \T1/ptm/m/n/10 Uncharger::uncharge() will now neu-tral-ize \T1/pcr/m/n/10 [Cl,B r,I][O-], [Cl,Br,I](=O)[O-], [Cl,Br, Underfull \hbox (badness 10000) in paragraph at lines 8641--8644 \T1/pcr/m/n/10 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 8641--8644 \T1/pcr/m/n/10 [N+](=O)([O-])[O-], P(=O)([O-])[O-], P(=O)([O-])([O-])[O-], S([O -])[O-], [134] [135] [136] Chapter 7. [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] Chapter 8. [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 10677. 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Underfull \hbox (badness 10000) in paragraph at lines 123--124 []\T1/ptm/m/n/10 Cheminformatics 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 217. [2] [3] [4] Chapter 2. [5] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [7] [8] [9] [10] Underfull \hbox (badness 10000) in paragraph at lines 746--747 []\T1/ptm/m/n/10 You can en-able sup-port for the Avalon toolkit by adding the ar-gu-ment [11] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 815. (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) Underfull \hbox (badness 10000) in paragraph at lines 844--845 []\T1/ptm/m/n/10 Add \T1/pcr/m/n/10 #define BOOST_PYTHON_NO_PY_SIGNATURES \T1/p tm/m/n/10 at the top of \T1/pcr/m/n/10 Code/GraphMol/Wrap/ [12] [13] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 951. Underfull \hbox (badness 10000) in paragraph at lines 951--952 \T1/pcr/m/n/10 installed to \T1/ptm/m/n/10 C:\boost\T1/pcr/m/n/10 , and that yo u will build the RDKit from a directory named Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 969. [14] Underfull \hbox (badness 10000) in paragraph at lines 991--992 []\T1/ptm/m/n/10 Run cmake. Here's an ex-am-ple ba-sic com-mand line for 64bit win-dows that will Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/ptm/m/n/10 down-load the InChI and Avalon toolkit sources from the InChI Tr ust and Source-Forge Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/ptm/m/n/10 repos-i-to-ries, re-spec-tively, and build the Post-greSQL car-t ridge for the in-stalled ver-sion Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/ptm/m/n/10 of Post-greSQL:\T1/pcr/m/n/10 cmake -DRDK_BUILD_PYTHON_WRAPPERS= ON -DBOOST_ROOT=C:/ Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/pcr/m/n/10 boost -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/pcr/m/n/10 -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\Postgre SQL\9.5" Underfull \hbox (badness 10000) in paragraph at lines 1000--1001 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" Underfull \hbox (badness 10000) in paragraph at lines 1006--1007 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" [15] [16] Chapter 3. [17] Underfull \hbox (badness 10000) in paragraph at lines 1102--1103 []\T1/ptm/m/n/10 displays a mes-sage like: \T1/pcr/m/n/10 [12:18:01] Explicit v alence for atom # 1 O greater than [18] [19] [20] [21] Overfull \vbox (1.28346pt too high) detected at line 1420 [22] [23] [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1652--1654 []\T1/ptm/m/n/10 Another op-tion for Com-pute2DCoords al-lows you to gen-er-ate 2D de-pic-tions for molecules that Underfull \hbox (badness 7649) in paragraph at lines 1652--1654 \T1/ptm/m/n/10 closely mimic 3D con-for-ma-tions. This is avail-able us-ing the func-tion \T1/pcr/m/n/10 rdkit.Chem.AllChem. [26 <./picture_1.png (PNG copy)> <./picture_0.png (PNG copy)> <./picture_3.png (PNG copy)>] Underfull \hbox (badness 10000) in paragraph at lines 1672--1677 []\T1/ptm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu nc-tion \T1/pcr/m/n/10 rdkit.Chem.rdDepictor. [27 <./picture_2.png> <./picture_4.png>] [28] [29] [30 <./cdk2_mol1.png> <./cdk 2_mol2.png>] [31 <./cdk2_molgrid.png (PNG copy)>] Underfull \vbox (badness 2707) detected at line 1972 [32 <./cdk2_molgrid_aligned.png (PNG copy)>] [33 <./atom_highlights_1.png>] [34 <./atom_highlights_2.png> <./atom_highlights_3.png>] [35 <./atom_annotation _1.png>] [36 <./atom_labels_1.png>] [37 <./atom_labels_2.png>] [38 <./atom_labe ls_3.png>] [39 <./mol_metadata1.png>] [40] [41] [42] [43 <./substruct_search_pa rameters1.png>] [44] [45] [46] [47] [48] [49] [50] [51] [52 <./mfp2_bit872.png> <./rdk_bit1553.png>] [53 <./rdk_bit1553_2.png>] [54] [55 <./similarity_map_fp1 .png>] [56 <./similarity_map_fp2.png>] [57 <./similarity_map_fp3.png>] [58] [59 <./similarity_map_charges.png>] [60 <./similarity_map_crippen.png>] [61] Overfull \hbox (59.44438pt too wide) in paragraph at lines 3309--3309 []\T1/pcr/m/n/9 [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- [62 <./reaction1.png>] [63 <./reaction1_highlight.png>] [64] [65] [66] [67] [68] [69] [70] Underfull \hbox (badness 6792) in paragraph at lines 3922--3925 []\T1/ptm/m/n/10 Or we can use the bit rank-ing func-tion-al-ity from the \T1/p cr/m/n/10 rdkit.ML.InfoTheory.rdInfoTheory. [71] [72] [73] [74 <./picture_6.png>] [75] Overfull \hbox (520.56647pt too wide) in alignment at lines 4193--4196 [] [] [] Overfull \hbox (520.56647pt too wide) in alignment at lines 4196--4202 [] [] [] Overfull \hbox (520.56647pt too wide) in alignment at lines 4202--4206 [] [] [] Overfull \hbox (520.56647pt too wide) in alignment at lines 4206--4208 [] [] [] Overfull \hbox (520.56647pt too wide) in alignment at lines 4208--4359 [] [] [] Overfull \hbox (520.56647pt too wide) in alignment at lines 4359--4509 [] [] [] Overfull \hbox (520.56647pt too wide) in alignment at lines 4509--4518 [] [] [] [76] Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 De-scrip- Overfull \hbox (19.3687pt too wide) in paragraph at lines 4661--4661 \T1/ptm/m/n/10 tor/Descriptor Overfull \hbox (3.88354pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 Lan- Overfull \hbox (8.88354pt too wide) in paragraph at lines 4661--4661 \T1/ptm/m/n/10 guage| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 \T1/ptm/m/n/10 best fit Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 PMI1, Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 \T1/ptm/m/n/10 PMI2, Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 NPR1, Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 Ra-dius Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 In-er-tial Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 \T1/ptm/m/n/10 shape Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 Ec-cen- Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 As- Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 Sphe-roc- Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 Au-to- Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 GET- Overfull \hbox (2.95337pt too wide) in paragraph at lines 4661--4661 []\T1/ptm/m/n/10 C++| [77] Underfull \hbox (badness 10000) in paragraph at lines 4750--4750 []\T1/ptm/m/n/10 Fin-ger-print Underfull \hbox (badness 10000) in paragraph at lines 4750--4750 []\T1/ptm/m/n/10 Lan- Overfull \hbox (2.77637pt too wide) in paragraph at lines 4750--4750 \T1/ptm/m/n/10 guage| Underfull \hbox (badness 10000) in paragraph at lines 4750--4750 []\T1/ptm/m/n/10 Topo-log-i-cal Underfull \hbox (badness 10000) in paragraph at lines 4750--4750 []\T1/ptm/m/n/10 Mor- Underfull \hbox (badness 10000) in paragraph at lines 4750--4750 []\T1/ptm/m/n/10 2D Phar-ma- Underfull \hbox (badness 10000) in paragraph at lines 4750--4750 []\T1/ptm/m/n/10 MHFP and [78] Overfull \hbox (0.97221pt too wide) in paragraph at lines 4800--4800 []\T1/ptm/m/n/10 Fea- Overfull \hbox (8.75237pt too wide) in paragraph at lines 4800--4800 []\T1/ptm/m/n/10 Donor| Underfull \hbox (badness 10000) in paragraph at lines 4800--4800 []\T1/ptm/m/n/10 Ac- Underfull \hbox (badness 10000) in paragraph at lines 4800--4800 []\T1/pcr/m/n/10 [$([O,S;H1;v2;!$(*-*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$( [N;v3;! 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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] Overfull \vbox (5.17178pt too high) detected at line 5258 [87] [88] [89] Underfull \hbox (badness 10000) in paragraph at lines 5644--5646 []\T1/ptm/m/n/10 metals, [90] [91 <./parastereo_2.png> <./parastereo_1.png>] [92 <./potential_stereo_dou ble_bond1.png> <./potential_stereo_double_bond2.png> <./potential_stereo_double _bond3.png>] [93] [94] [95] [96] [97] [98] [99] [100] [101 <./picture_10.jpg>] Overfull \vbox (2.72571pt too high) detected at line 6557 [102] [103] Underfull \hbox (badness 10000) in paragraph at lines 6787--6787 []\T1/ptm/m/n/10 _Chi-ral-i-ty-Pos-si- Underfull \hbox (badness 10000) in paragraph at lines 6787--6787 []\T1/ptm/m/n/10 _Re-ac-tion-De- Underfull \hbox (badness 10000) in paragraph at lines 6787--6787 []\T1/ptm/m/n/10 mo-lAtomMap- Underfull \hbox (badness 10000) in paragraph at lines 6787--6787 []\T1/ptm/m/n/10 molFileIn-ver- Underfull \hbox (badness 10000) in paragraph at lines 6787--6787 []\T1/ptm/m/n/10 mol-Rxn-Com-po- [104] [105] Underfull \hbox (badness 10000) in paragraph at lines 6926--6930 []\T1/ptm/m/n/10 By de-fault the \T1/pcr/m/n/10 rdkit.Chem.rdmolfiles.SDMolSupp lier \T1/ptm/m/n/10 and \T1/pcr/m/n/10 rdkit.Chem.rdmolfiles. Underfull \hbox (badness 6559) in paragraph at lines 6926--6930 \T1/pcr/m/n/10 ForwardSDMolSupplier \T1/ptm/m/n/10 classes (\T1/pcr/m/n/10 RDKi t::SDMolSupplier \T1/ptm/m/n/10 and \T1/pcr/m/n/10 RDKit::ForwardMolSupplier [106] Underfull \hbox (badness 10000) in paragraph at lines 6975--6978 []\T1/ptm/m/n/10 If you have atom prop-er-ties that you would like to have writ -ten to SDF files, you can Underfull \hbox (badness 10000) in paragraph at lines 6975--6978 \T1/ptm/m/n/10 use the func-tions \T1/pcr/m/n/10 rdkit.Chem.rdmolfiles.CreateAt omStringPropertyList()\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6975--6978 \T1/pcr/m/n/10 rdkit.Chem.rdmolfiles.CreateAtomIntPropertyList()\T1/ptm/m/n/10 , \T1/pcr/m/n/10 rdkit.Chem. Underfull \hbox (badness 10000) in paragraph at lines 6975--6978 \T1/pcr/m/n/10 rdmolfiles.CreateAtomDoublePropertyList()\T1/ptm/m/n/10 , or \T1 /pcr/m/n/10 rdkit.Chem.rdmolfiles. [107] Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/phv/m/n/10 Mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- [108] [109 <./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 7558) in paragraph at lines 7102--7104 []\T1/ptm/m/n/10 It is pos-si-ble to enu-mer-ate the el-e-ments of a \T1/pcr/m/ n/10 StereoGroup \T1/ptm/m/n/10 us-ing the func-tion \T1/pcr/m/n/10 rdkit.Chem. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Underfull \hbox (badness 10000) in paragraph at lines 7116--7117 []\T1/ptm/m/n/10 Reactions also pre-serve \T1/pcr/m/n/10 StereoGroup\TS1/cmtt/m /n/10 ``\T1/pcr/m/n/10 s. Product atoms are included in the Underfull \hbox (badness 10000) in paragraph at lines 7159--7161 [] Underfull \hbox (badness 10000) in paragraph at lines 7270--7272 [] [110] [111 <./EnhancedStereoSSS_molA.png> <./EnhancedStereoSSS_molB.png> <./Enh ancedStereoSSS_molC.png> <./EnhancedStereoSSS_molD.png> <./EnhancedStereoSSS_mo lE.png> <./EnhancedStereoSSS_molF.png> <./EnhancedStereoSSS_molG.png>] [112] [113] [114] Chapter 5. [115] [116] [117] [118] Overfull \hbox (1096.24321pt too wide) in paragraph at lines 7756--7756 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][ ]2[]CCCN2C([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O) [C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]([C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)CC)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CO)NC([]=[]O)[C[]\T1/pcr /b/n/9 @H[]\T1/pcr/m/n/9 ](C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]([C []\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)O)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T 1/pcr/m/n/9 ][]2[]CSSC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](NC1[]=[]O)C([]=[]O) N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1cnc[nH][]1[])C([]=[]O)N[C[]\T1/p cr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1 /pcr/m/n/9 ](CCCNC([]=[]N)N)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1c[nH]c3ccccc13)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC( []=[]N)N)C([]=[]O)N2| Overfull \hbox (167.44426pt too wide) in paragraph at lines 7758--7758 []\T1/pcr/m/n/9 CN1C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC([]=[]N) N)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccc(O)cc2)NC([]=[]O)[ C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @ H[]\T1/pcr/m/n/9 ](Cc2ccc3ccccc3c2)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr /m/n/9 ][]1[]CC([]=[]O)O| Overfull \hbox (113.44432pt too wide) in paragraph at lines 7759--7759 []\T1/pcr/m/n/9 NCCCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](NC([]=[]O)[C[]\T1/pc r/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccc(OP([]=[]O)(O)O)cc1)NC([]=[]O)Cc1ccccc1)C([]= []O)N1CCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[]O)N[C[]@[][]\T1/pcr/b /n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C(N)[]=[]O| Overfull \hbox (675.04369pt too wide) in paragraph at lines 7760--7760 []\T1/pcr/m/n/9 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Underfull \hbox (badness 10000) in paragraph at lines 123--124 []\T1/ptm/m/n/10 Cheminformatics 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 217. [2] [3] [4] Chapter 2. [5] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [7] [8] [9] [10] Underfull \hbox (badness 10000) in paragraph at lines 746--747 []\T1/ptm/m/n/10 You can en-able sup-port for the Avalon toolkit by adding the ar-gu-ment [11] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 815. 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Here's an ex-am-ple ba-sic com-mand line for 64bit win-dows that will Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/ptm/m/n/10 down-load the InChI and Avalon toolkit sources from the InChI Tr ust and Source-Forge Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/ptm/m/n/10 repos-i-to-ries, re-spec-tively, and build the Post-greSQL car-t ridge for the in-stalled ver-sion Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/ptm/m/n/10 of Post-greSQL:\T1/pcr/m/n/10 cmake -DRDK_BUILD_PYTHON_WRAPPERS= ON -DBOOST_ROOT=C:/ Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/pcr/m/n/10 boost -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 991--992 \T1/pcr/m/n/10 -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\Postgre SQL\9.5" Underfull \hbox (badness 10000) in paragraph at lines 1000--1001 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" Underfull \hbox (badness 10000) in paragraph at lines 1006--1007 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" [15] [16] Chapter 3. [17] Underfull \hbox (badness 10000) in paragraph at lines 1102--1103 []\T1/ptm/m/n/10 displays a mes-sage like: \T1/pcr/m/n/10 [12:18:01] Explicit v alence for atom # 1 O greater than [18] [19] [20] [21] Overfull \vbox (1.28346pt too high) detected at line 1420 [22] [23] [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1652--1654 []\T1/ptm/m/n/10 Another op-tion for Com-pute2DCoords al-lows you to gen-er-ate 2D de-pic-tions for molecules that Underfull \hbox (badness 7649) in paragraph at lines 1652--1654 \T1/ptm/m/n/10 closely mimic 3D con-for-ma-tions. This is avail-able us-ing the func-tion \T1/pcr/m/n/10 rdkit.Chem.AllChem. [26 <./picture_1.png (PNG copy)> <./picture_0.png (PNG copy)> <./picture_3.png (PNG copy)>] Underfull \hbox (badness 10000) in paragraph at lines 1672--1677 []\T1/ptm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu nc-tion \T1/pcr/m/n/10 rdkit.Chem.rdDepictor. 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[107] Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/phv/m/n/10 Mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 7087--7087 []\T1/ptm/m/n/10 mix- [108] [109 <./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 7558) in paragraph at lines 7102--7104 []\T1/ptm/m/n/10 It is pos-si-ble to enu-mer-ate the el-e-ments of a \T1/pcr/m/ n/10 StereoGroup \T1/ptm/m/n/10 us-ing the func-tion \T1/pcr/m/n/10 rdkit.Chem. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 1. Underfull \hbox (badness 10000) in paragraph at lines 7116--7117 []\T1/ptm/m/n/10 Reactions also pre-serve \T1/pcr/m/n/10 StereoGroup\TS1/cmtt/m /n/10 ``\T1/pcr/m/n/10 s. Product atoms are included in the Underfull \hbox (badness 10000) in paragraph at lines 7159--7161 [] Underfull \hbox (badness 10000) in paragraph at lines 7270--7272 [] [110] [111 <./EnhancedStereoSSS_molA.png> <./EnhancedStereoSSS_molB.png> <./Enh ancedStereoSSS_molC.png> <./EnhancedStereoSSS_molD.png> <./EnhancedStereoSSS_mo lE.png> <./EnhancedStereoSSS_molF.png> <./EnhancedStereoSSS_molG.png>] [112] [113] [114] Chapter 5. [115] [116] [117] [118] Overfull \hbox (1096.24321pt too wide) in paragraph at lines 7756--7756 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][ ]2[]CCCN2C([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O) [C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]([C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)CC)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CO)NC([]=[]O)[C[]\T1/pcr /b/n/9 @H[]\T1/pcr/m/n/9 ](C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]([C []\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)O)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T 1/pcr/m/n/9 ][]2[]CSSC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](NC1[]=[]O)C([]=[]O) N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1cnc[nH][]1[])C([]=[]O)N[C[]\T1/p cr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1 /pcr/m/n/9 ](CCCNC([]=[]N)N)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1c[nH]c3ccccc13)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC( []=[]N)N)C([]=[]O)N2| Overfull \hbox (167.44426pt too wide) in paragraph at lines 7758--7758 []\T1/pcr/m/n/9 CN1C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC([]=[]N) N)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccc(O)cc2)NC([]=[]O)[ C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @ H[]\T1/pcr/m/n/9 ](Cc2ccc3ccccc3c2)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr /m/n/9 ][]1[]CC([]=[]O)O| Overfull \hbox (113.44432pt too wide) in paragraph at lines 7759--7759 []\T1/pcr/m/n/9 NCCCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](NC([]=[]O)[C[]\T1/pc r/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccc(OP([]=[]O)(O)O)cc1)NC([]=[]O)Cc1ccccc1)C([]= []O)N1CCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[]O)N[C[]@[][]\T1/pcr/b /n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C(N)[]=[]O| Overfull \hbox (675.04369pt too wide) in paragraph at lines 7760--7760 []\T1/pcr/m/n/9 CCCCCCCCCCCCCCCCNC([]=[]O)CN(CC([]=[]O)NC(C)(C)C([]=[]O)N[C[]@[ ][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC([]=[]N)N )C([]=[]O)N1CCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[]O)N[C[]@[][]\T1 /pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC([]=[]N)N)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(N)[]=[]O)C(N)[]=[]O)C([]=[]O)c1cccnc1| Overfull \hbox (491.4439pt too wide) in paragraph at lines 7761--7761 []\T1/pcr/m/n/9 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 (383.44402pt too wide) in paragraph at lines 7762--7762 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2cc ccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]@[][] \T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/p cr/m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C(C)C)NC([ ]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCSC)NC1[]=[]O| Overfull \hbox (394.244pt too wide) in paragraph at lines 7763--7763 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2cc ccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]@[][] \T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/p cr/m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C(C)C)NC([ ]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 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@H[]\T1/pcr/m/n/9 ][]2[]CCC N2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC[S[]+[]](C)[O[]- [119] Overfull \hbox (1096.24321pt too wide) in paragraph at lines 7778--7778 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][ ]2[]CCCN2C([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O) [C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]([C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)CC)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CO)NC([]=[]O)[C[]\T1/pcr /b/n/9 @H[]\T1/pcr/m/n/9 ](C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]([C []\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)O)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T 1/pcr/m/n/9 ][]2[]CSSC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](NC1[]=[]O)C([]=[]O) N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1cnc[nH][]1[])C([]=[]O)N[C[]\T1/p cr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1 /pcr/m/n/9 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lines 7782--7782 []\T1/pcr/m/n/9 CCCCCCCCCCCCCCCCNC([]=[]O)CN(CC([]=[]O)NC(C)(C)C([]=[]O)N[C[]@[ ][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC([]=[]N)N )C([]=[]O)N1CCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[]O)N[C[]@[][]\T1 /pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCNC([]=[]N)N)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(N)[]=[]O)C(N)[]=[]O)C([]=[]O)c1cccnc1| Overfull \hbox (383.44402pt too wide) in paragraph at lines 7783--7783 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2cc ccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]@[][] \T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/p cr/m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C(C)C)NC([ ]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCSC)NC1[]=[]O| Overfull \hbox (394.244pt too wide) in paragraph at lines 7784--7784 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2cc ccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]@[][] \T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/p cr/m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C(C)C)NC([ ]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC[S[]+[]](C)[O[]- Overfull \hbox (448.24394pt too wide) in paragraph at lines 7785--7785 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2c[ nH]c3ccccc23)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccccc2)NC([]=[] O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]@[][]\T1/pcr/b/ n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ] (CCSC)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)NC([]=[]O)[C[]\T1/ pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC[S[]+[]](C)[O[]- Overfull \hbox (270.04414pt too wide) in paragraph at lines 7786--7786 [][]\T1/pcr/m/n/9 ])NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C(C)C)NC([] =[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2c[nH]c3ccccc23)NC([]=[]O)[C[]\T1/ pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr /m/n/9 ](Cc2ccccc2)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCC N2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC[S[]+[]](C)[O[]- Overfull \hbox (550.84383pt too wide) in paragraph at lines 7787--7787 []\T1/pcr/m/n/9 CC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)[C[]\T1/pcr/b/n/9 @H[ ]\T1/pcr/m/n/9 ](N)C([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C([]=[]O)N[C []@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)C([]=[]O)N[C[]\T1/pcr/b/n/9 @H[ ]\T1/pcr/m/n/9 ](C([]=[]O)N1CCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[ ]O)N1CCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[]O)N[C[]\T1/pcr/b/n/9 @ H[]\T1/pcr/m/n/9 ](CCC([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCC([ ]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CC(C)C)C([]=[]O)O)Cc1ccccc1)C c1ccccc1)C(C)C)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)CC| [120] [121] [122] Overfull \vbox (1.18257pt too high) detected at line 7995 [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] Chapter 6. [133] Underfull \hbox (badness 10000) in paragraph at lines 8641--8644 \T1/ptm/m/n/10 Uncharger::uncharge() will now neu-tral-ize \T1/pcr/m/n/10 [Cl,B r,I][O-], [Cl,Br,I](=O)[O-], [Cl,Br, Underfull \hbox (badness 10000) in paragraph at lines 8641--8644 \T1/pcr/m/n/10 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 8641--8644 \T1/pcr/m/n/10 [N+](=O)([O-])[O-], P(=O)([O-])[O-], P(=O)([O-])([O-])[O-], S([O -])[O-], [134] [135] [136] Chapter 7. [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] Chapter 8. [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family ptm in TS1 encoding. (textcomp) Default family used instead on input line 10677. Underfull \hbox (badness 10000) in paragraph at lines 10677--10678 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 auto\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 keywor d here is hiding the fact that \T1/ptm/m/n/10 get-Bond-Be-tweenAtoms\T1/pcr/m/n /10 returns the [165] LaTeX Warning: Hyper reference `GettingStartedInC++:TheSSSRProblem' on page 166 undefined on input line 10793. [166] LaTeX Warning: Hyper reference `GettingStartedInC++:twoAddHs' on page 167 undef ined on input line 10820. [167] [168] LaTeX Warning: Hyper reference `GettingStartedInC++:blaney' on page 169 undefin ed on input line 10993. LaTeX Warning: Hyper reference `GettingStartedInC++:rappe' on page 169 undefine d on input line 11022. LaTeX Warning: Hyper reference `GettingStartedInC++:riniker2' on page 169 undef ined on input line 11025. [169] LaTeX Warning: Hyper reference `GettingStartedInC++:mmff1' on page 170 undefine d on input line 11066. LaTeX Warning: Hyper reference `GettingStartedInC++:mmff2' on page 170 undefine d on input line 11066. LaTeX Warning: Hyper reference `GettingStartedInC++:mmff3' on page 170 undefine d on input line 11066. LaTeX Warning: Hyper reference `GettingStartedInC++:mmff4' on page 170 undefine d on input line 11067. LaTeX Warning: Hyper reference `GettingStartedInC++:mmffs' on page 170 undefine d on input line 11067. [170] Overfull \vbox (2.2835pt too high) detected at line 11220 [171] [172] [173] [174] [175] [176] LaTeX Warning: Hyper reference `GettingStartedInC++:guba' on page 177 undefined on input line 11588. [177] [178] [179] [180] Chapter 9. [181] [182] Chapter 10. (./RDKit.ind) [183] (./RDKit.aux) LaTeX Warning: There were undefined references. ) (see the transcript file for additional information) {/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8 r.enc} Output written on RDKit.pdf (191 pages, 1671546 bytes). Transcript written on RDKit.log. Latexmk: Index file 'RDKit.idx' was written Latexmk: Log file says output to 'RDKit.pdf' Latexmk: Examining 'RDKit.log' === TeX engine is 'pdfTeX' Latexmk: All targets (RDKit.pdf) are up-to-date make[3]: Leaving directory '/build/reproducible-path/rdkit-202009.4/Docs/Book/_build/latex' pdflatex finished; the PDF files are in _build/latex. make[2]: Leaving directory '/build/reproducible-path/rdkit-202009.4/Docs/Book' make[1]: Leaving directory '/build/reproducible-path/rdkit-202009.4' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/rdkit-202009.4' cp -r rdkit obj-*/ find /build/reproducible-path/rdkit-202009.4 -name rdchem.so /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/rdkit/Chem/rdchem.so #export RDBASE=/build/reproducible-path/rdkit-202009.4 PYTHONPATH=/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu//lib:/usr/lib/libeatmydata" PYTHONPATH=/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/:/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu//lib:/usr/lib/libeatmydata" dh_auto_test dh_auto_test: warning: Compatibility levels before 10 are deprecated (level 9 in use) cd obj-i686-linux-gnu && make -j15 test ARGS\+=-j15 make[2]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process -j15 Test project /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu Start 1: testCoordGen Start 2: pyCoordGen Start 3: testDict Start 4: testRDValue Start 5: testConcurrentQueue Start 6: testDataStructs Start 7: testFPB Start 8: testMultiFPB Start 9: pyBV Start 10: pyDiscreteValueVect Start 11: pySparseIntVect Start 12: pyFPB Start 13: testTransforms Start 14: testGrid Start 15: geometryTestsCatch 1/190 Test #4: testRDValue ............................ Passed 0.02 sec Start 16: testPyGeometry 2/190 Test #6: testDataStructs ........................ Passed 0.02 sec Start 17: testMatrices 3/190 Test #7: testFPB ................................ Passed 0.02 sec Start 18: testConrec 4/190 Test #8: testMultiFPB ........................... Passed 0.02 sec Start 19: testAlignment 5/190 Test #13: testTransforms ......................... Passed 0.02 sec Start 20: pyAlignment 6/190 Test #15: geometryTestsCatch ..................... Passed 0.02 sec Start 21: testOptimizer 7/190 Test #17: testMatrices ........................... Passed 0.01 sec Start 22: testUFFForceField 8/190 Test #19: testAlignment .......................... Passed 0.01 sec Start 23: testMMFFForceField 9/190 Test #18: testConrec ............................. Passed 0.02 sec Start 24: pyForceFieldConstraints 10/190 Test #21: testOptimizer .......................... Passed 0.01 sec Start 25: testDistGeom 11/190 Test #14: testGrid ............................... Passed 0.04 sec Start 26: pyDistGeom 12/190 Test #25: testDistGeom ........................... Passed 0.02 sec Start 27: graphmolTest1 13/190 Test #22: testUFFForceField ...................... Passed 0.11 sec Start 28: graphmolcpTest 14/190 Test #28: graphmolcpTest ......................... Passed 0.02 sec Start 29: graphmolqueryTest 15/190 Test #29: graphmolqueryTest ...................... Passed 0.03 sec Start 30: graphmolMolOpsTest 16/190 Test #11: pySparseIntVect ........................ Passed 0.27 sec Start 31: graphmoltestChirality 17/190 Test #10: pyDiscreteValueVect .................... Passed 0.27 sec Start 32: graphmoltestPickler 18/190 Test #20: pyAlignment ............................ Passed 0.26 sec Start 33: graphmoltestPicklerGlobalSetting 19/190 Test #12: pyFPB .................................. Passed 0.28 sec Start 34: graphmolIterTest 20/190 Test #26: pyDistGeom ............................. Passed 0.25 sec Start 35: hanoiTest 21/190 Test #34: graphmolIterTest ....................... Passed 0.02 sec Start 36: graphmolMemTest1 22/190 Test #16: testPyGeometry ......................... Passed 0.30 sec Start 37: resMolSupplierTest 23/190 Test #33: graphmoltestPicklerGlobalSetting ....... Passed 0.03 sec Start 38: molBundleTest 24/190 Test #36: graphmolMemTest1 ....................... Passed 0.01 sec Start 39: testSGroup 25/190 Test #38: molBundleTest .......................... Passed 0.03 sec Start 40: test-valgrind 26/190 Test #39: testSGroup ............................. Passed 0.04 sec Start 41: graphmolTestsCatch 27/190 Test #31: graphmoltestChirality .................. Passed 0.09 sec Start 42: graphmolSGroupCatch 28/190 Test #40: test-valgrind .......................... Passed 0.03 sec Start 43: graphmolAdjustQueryCatch 29/190 Test #42: graphmolSGroupCatch .................... Passed 0.03 sec Start 44: chiralityTestsCatch 30/190 Test #41: graphmolTestsCatch ..................... Passed 0.05 sec Start 45: testDepictor 31/190 Test #2: pyCoordGen ............................. Passed 0.44 sec Start 46: pyDepictor 32/190 Test #43: graphmolAdjustQueryCatch ............... Passed 0.06 sec Start 47: smiTest1 33/190 Test #44: chiralityTestsCatch .................... Passed 0.04 sec Start 48: smiTest2 34/190 Test #1: testCoordGen ........................... Passed 0.47 sec Start 49: cxsmilesTest 35/190 Test #48: smiTest2 ............................... Passed 0.02 sec Start 50: smaTest1 36/190 Test #49: cxsmilesTest ........................... Passed 0.03 sec Start 51: smiTestCatch 37/190 Test #51: smiTestCatch ........................... Passed 0.05 sec Start 52: fileParsersTest1 38/190 Test #32: graphmoltestPickler .................... Passed 0.28 sec Start 53: testMolSupplier 39/190 Test #50: smaTest1 ............................... Passed 0.17 sec Start 54: testGeneralFileReader 40/190 Test #47: smiTest1 ............................... Passed 0.23 sec Start 55: testMultithreadedMolSupplier 41/190 Test #45: testDepictor ........................... Passed 0.33 sec Start 56: testMolWriter 42/190 Test #54: testGeneralFileReader .................. Passed 0.13 sec Start 57: testTplParser 43/190 Test #57: testTplParser .......................... Passed 0.04 sec Start 58: testMol2ToMol 44/190 Test #9: pyBV ................................... Passed 0.83 sec Start 59: testSequence 45/190 Test #58: testMol2ToMol .......................... Passed 0.05 sec Start 60: testExtendedStereoParsing 46/190 Test #59: testSequence ........................... Passed 0.05 sec Start 61: fileParsersCatchTest 47/190 Test #60: testExtendedStereoParsing .............. Passed 0.04 sec Start 62: testPropertyLists 48/190 Test #53: testMolSupplier ........................ Passed 0.33 sec Start 63: testSubstructMatch 49/190 Test #46: pyDepictor ............................. Passed 0.50 sec Start 64: substructTestCatch 50/190 Test #62: testPropertyLists ...................... Passed 0.04 sec Start 65: testReaction 51/190 Test #61: fileParsersCatchTest ................... Passed 0.07 sec Start 66: testReactionFingerprints 52/190 Test #24: pyForceFieldConstraints ................ Passed 0.93 sec Start 67: testEnumeration 53/190 Test #64: substructTestCatch ..................... Passed 0.06 sec Start 68: rxnTestCatch 54/190 Test #66: testReactionFingerprints ............... Passed 0.07 sec Start 69: pyChemReactions 55/190 Test #68: rxnTestCatch ........................... Passed 0.09 sec Start 70: pyChemReactionEnumerations 56/190 Test #56: testMolWriter .......................... Passed 0.36 sec Start 71: pyChemReactionSanitize 57/190 Test #63: testSubstructMatch ..................... Passed 0.46 sec Start 72: testChemTransforms 58/190 Test #71: pyChemReactionSanitize ................. Passed 0.33 sec Start 73: chemTransformsTestCatch 59/190 Test #72: testChemTransforms ..................... Passed 0.10 sec Start 74: tautomerQueryTestCatch 60/190 Test #73: chemTransformsTestCatch ................ Passed 0.03 sec Start 75: pyTautomerQuery 61/190 Test #65: testReaction ........................... Passed 0.55 sec Start 76: testSubgraphs1 62/190 Test #30: graphmolMolOpsTest ..................... Passed 1.29 sec Start 77: testSubgraphs2 63/190 Test #77: testSubgraphs2 ......................... Passed 0.03 sec Start 78: filterCatalogTest 64/190 Test #74: tautomerQueryTestCatch ................. Passed 0.15 sec Start 79: pyFilterCatalog 65/190 Test #69: pyChemReactions ........................ Passed 0.61 sec Start 80: testFragCatalog 66/190 Test #78: filterCatalogTest ...................... Passed 0.22 sec Start 81: pyFragCatalog 67/190 Test #75: pyTautomerQuery ........................ Passed 0.32 sec Start 82: testDescriptors 68/190 Test #76: testSubgraphs1 ......................... Passed 0.42 sec Start 83: testAUTOCORR2D 69/190 Test #3: testDict ............................... Passed 2.09 sec Start 84: testATF 70/190 Test #81: pyFragCatalog .......................... Passed 0.36 sec Start 85: testBCUT 71/190 Test #84: testATF ................................ Passed 0.04 sec Start 86: testEEM 72/190 Test #83: testAUTOCORR2D ......................... Passed 0.44 sec Start 87: testPBF 73/190 Test #80: testFragCatalog ........................ Passed 0.94 sec Start 88: testRDFcustom 74/190 Test #87: testPBF ................................ Passed 0.30 sec Start 89: testRDF 75/190 Test #86: testEEM ................................ Passed 0.81 sec Start 90: testMORSE 76/190 Test #79: pyFilterCatalog ........................ Passed 1.46 sec Start 91: test3D 77/190 Test #85: testBCUT ............................... Passed 1.09 sec Start 92: testWHIM 78/190 Test #92: testWHIM ............................... Passed 0.39 sec Start 93: testGETAWAY 79/190 Test #91: test3D ................................. Passed 0.92 sec Start 94: testAUTOCORR3D 80/190 Test #90: testMORSE .............................. Passed 1.05 sec Start 95: testCoulombMat 81/190 Test #95: testCoulombMat ......................... Passed 0.06 sec Start 96: pyMolDescriptors 82/190 Test #70: pyChemReactionEnumerations ............. Passed 3.01 sec Start 97: pyMolDescriptors3D 83/190 Test #37: resMolSupplierTest ..................... Passed 3.78 sec Start 98: testFingerprints 84/190 Test #35: hanoiTest .............................. Passed 3.94 sec Start 99: testMHFPFingerprint 85/190 Test #99: testMHFPFingerprint .................... Passed 0.08 sec Start 100: testFingerprintGenerators 86/190 Test #96: pyMolDescriptors ....................... Passed 0.43 sec Start 101: fpTestCatch 87/190 Test #94: testAUTOCORR3D ......................... Passed 0.56 sec Start 102: pyTestGenerator 88/190 Test #101: fpTestCatch ............................ Passed 0.07 sec Start 103: pyTestMHFP 89/190 Test #82: testDescriptors ........................ Passed 2.84 sec Start 104: testPartialCharges 90/190 Test #104: testPartialCharges ..................... Passed 0.03 sec Start 105: pyPartialCharges 91/190 Test #97: pyMolDescriptors3D ..................... Passed 0.58 sec Start 106: testMolTransforms 92/190 Test #106: testMolTransforms ...................... Passed 0.08 sec Start 107: pyMolTransforms 93/190 Test #102: pyTestGenerator ........................ Passed 0.29 sec Start 108: testMMFFForceFieldHelpers 94/190 Test #103: pyTestMHFP ............................. Passed 0.30 sec Start 109: testMMFFForceFieldHelpersMultiThread 95/190 Test #105: pyPartialCharges ....................... Passed 0.43 sec Start 110: testUFFForceFieldHelpers 96/190 Test #107: pyMolTransforms ........................ Passed 0.37 sec Start 111: testCrystalForceField 97/190 Test #111: testCrystalForceField .................. Passed 0.14 sec Start 112: pyForceFieldHelpers 98/190 Test #100: testFingerprintGenerators .............. Passed 1.06 sec Start 113: testDistGeomHelpers 99/190 Test #109: testMMFFForceFieldHelpersMultiThread ... Passed 0.55 sec Start 114: pyDistGeomHelpers 100/190 Test #112: pyForceFieldHelpers .................... Passed 0.46 sec Start 115: testMolAlign 101/190 Test #89: testRDF ................................ Passed 3.11 sec Start 116: testO3AAlign 102/190 Test #115: testMolAlign ........................... Passed 0.19 sec Start 117: pyMolAlign 103/190 Test #93: testGETAWAY ............................ Passed 3.17 sec Start 118: testFeatures 104/190 Test #118: testFeatures ........................... Passed 0.05 sec Start 119: pyChemicalFeatures 105/190 Test #119: pyChemicalFeatures ..................... Passed 0.40 sec Start 120: testShapeHelpers 106/190 Test #120: testShapeHelpers ....................... Passed 0.05 sec Start 121: pyShapeHelpers 107/190 Test #121: pyShapeHelpers ......................... Passed 0.40 sec Start 122: testMolCatalog 108/190 Test #122: testMolCatalog ......................... Passed 0.07 sec Start 123: pyMolCatalog 109/190 Test #123: pyMolCatalog ........................... Passed 0.53 sec Start 124: moldraw2DTest1 110/190 Test #55: testMultithreadedMolSupplier ........... Passed 7.62 sec Start 125: moldraw2DTestCatch 111/190 Test #125: moldraw2DTestCatch ..................... Passed 0.33 sec Start 126: moldraw2DRxnTest1 112/190 Test #52: fileParsersTest1 ....................... Passed 8.37 sec Start 127: pyMolDraw2D 113/190 Test #126: moldraw2DRxnTest1 ...................... Passed 0.47 sec Start 128: testFMCS 114/190 Test #108: testMMFFForceFieldHelpers .............. Passed 4.90 sec Start 129: pyFMCS 115/190 Test #127: pyMolDraw2D ............................ Passed 1.04 sec Start 130: FMCStest 116/190 Test #130: FMCStest ............................... Passed 0.07 sec Start 131: molHashCatchTest 117/190 Test #131: molHashCatchTest ....................... Passed 0.09 sec Start 132: pyMolHash 118/190 Test #110: testUFFForceFieldHelpers ............... Passed 5.27 sec Start 133: testMMPA 119/190 Test #132: pyMolHash .............................. Passed 0.31 sec Start 134: pyMMPA 120/190 Test #98: testFingerprints ....................... Passed 6.41 sec Start 135: testCIPLabeler 121/190 Test #133: testMMPA ............................... Passed 0.24 sec Start 136: pyCIPLabelsWrapTest 122/190 Test #135: testCIPLabeler ......................... Passed 0.12 sec Start 137: pyCIPLabelsValidation 123/190 Test #136: pyCIPLabelsWrapTest .................... Passed 0.39 sec Start 138: deprotectTest 124/190 Test #138: deprotectTest .......................... Passed 0.19 sec Start 139: pyDeprotect 125/190 Test #139: pyDeprotect ............................ Passed 0.48 sec Start 140: testReducedGraphs 126/190 Test #140: testReducedGraphs ...................... Passed 0.10 sec Start 141: pyReducedGraphs 127/190 Test #141: pyReducedGraphs ........................ Passed 0.41 sec Start 142: trajectoryTest 128/190 Test #134: pyMMPA ................................. Passed 2.02 sec Start 143: substructLibraryTest 129/190 Test #128: testFMCS ...............................Child aborted***Exception: 3.52 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 0.182 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 0.036 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 0.074 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 0.383 seconds testSimple() MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds Time elapsed 0.213 seconds MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds Time elapsed 0.146 seconds MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds Time elapsed 0.147 seconds testSegFault() MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds Time elapsed 0.012 seconds MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds Time elapsed 0.014 seconds MCS MatchFusedRingsStrict: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds Time elapsed 0.016 seconds testThreshold() MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds Time elapsed 0.000 seconds testRing1() MCS: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds Time elapsed 0.988 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 0.333 seconds MCS MatchFusedRingsStrict: [#6]1:&@[#6]:&@[#7]:&@[#6](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds Time elapsed 0.355 seconds testAtomCompareIsotopes() MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds Time elapsed 0.004 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 test18() Query +MAP [CH3:0][c:1]1[n:2][c:3]([CH2:4][N:5]([CH:6]([CH3:7])[c:8]2[n:9][cH:10][cH:11][cH:12][cH:13]2)[CH2:14][CH2:15][CH2:16][CH2:17][NH2:18])[cH:19][cH:20][cH:21]1 MCS: [#6](:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#7]:[#6]:[#6]:[#6]:[#6]:1)-[#6]-[#6]-[#6]-[#6]-[#7]):[#6]:[#6]:[#6] 21 atoms, 21 bonds Time elapsed 0.010 seconds test504() Query +MAP [CH2:0]([CH2:1][CH2:2][NH:3][C:4]([CH:5]1[CH2:6][CH:7]1[c:8]1[c:9][c:10]([Cl:11])[c:12]([Cl:13])[cH:14][c:15]1)=[O:16])[CH2:17][CH2:18][N:19]1[CH2:20][CH2:21][CH:22]([NH:23][C:24]([NH:25][c:26]2[cH:27][cH:28][c:29]([Cl:30])[cH:31][cH:32]2)=[O:33])[CH2:34]1 MCS: [#6](-[#6]-[#6]-[#7]-[#6](-[#6]1-[#6]-[#6]-1-[#6]1:[#6]:[#6](-[#17]):[#6](:[#6]:[#6]:1)-[#17])=[#8])-[#6]-[#6]-[#7](-[#6]-[#6]-[#6]-[#7]-[#6](-[#7]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)=[#8])-[#6] 34 atoms, 36 bonds Time elapsed 0.126 seconds MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds Time elapsed 0.002 seconds MCS: [#6]1-[#6]-[#7]-[#6](-[#6]-[#7]-1-[#6]1:[#6](:[#6]:[#6]2:[#6](:[#6](:[#6]:[#7](-[#6]3-[#6]-[#6]-3):[#6]:2:[#6]:1)-[#6](=[#8])-[#8])=[#8])-[#9])-[#6] 25 atoms, 28 bonds Time elapsed 0.036 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 0.0014 seconds. bond[0]=6 STATISTICS: Total Growing Steps = 1, MCS found on 1 step, for 0.0014 seconds Initial Seeds = 1, Mismatched 0 Inspected Seeds = 2 Rejected by BestSize = 0 SingleBondExcluded = 0 MatchCheck Seeds = 2 MatchCalls = 2 MatchFound = 1 fastMatchCalls = 1 fastMatchFound = 0 slowMatchCalls = 2 slowMatchFound = 1 DupCacheFound = 0 0 matched, 0 mismatched HashCache size = 1 keys HashCache size = 1 entries FindHashInCache = 2 HashFoundInCache= 0 ExactMatchCalls = 0 ExactMatchFound = 0 Time elapsed 0.002 seconds query=OCCl SubstructMatch(useChirality=false) res =1 size=3 query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 test target = O[C@H](F)CCl query = C(F)C useChirality = 0 res sub = 1 size=3 MCS: [#9]-[#6]-[#6] 3 atoms, 2 bonds test target = O[C@H](F)CCl query = C(F)C useChirality = 1 res sub = 1 size=3 MCS: [#9]-[#6]-[#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 terminate called after throwing an instance of 'Invar::Invariant' what(): Expression Failed: Start 144: pySubstructLibrary 130/190 Test #142: trajectoryTest ......................... Passed 0.63 sec Start 145: testRGroupDecomp 131/190 Test #88: testRDFcustom .......................... Passed 10.53 sec Start 146: pyRGroupDecomposition 132/190 Test #67: testEnumeration ........................ Passed 12.91 sec Start 147: molInterchangeTest1 133/190 Test #147: molInterchangeTest1 .................... Passed 0.04 sec Start 148: pyMolInterchange 134/190 Test #148: pyMolInterchange ....................... Passed 0.28 sec Start 149: testSLNParse 135/190 Test #149: testSLNParse ........................... Passed 0.08 sec Start 150: pySLNParse 136/190 Test #124: moldraw2DTest1 ......................... Passed 6.05 sec Start 151: pyGraphMolWrap 137/190 Test #150: pySLNParse ............................. Passed 0.32 sec Start 152: pyTestConformerWrap 138/190 Test #129: pyFMCS ................................. Passed 4.97 sec Start 153: pyTestTrajectory 139/190 Test #152: pyTestConformerWrap .................... Passed 0.53 sec Start 154: pyTestSGroups 140/190 Test #153: pyTestTrajectory ....................... Passed 0.72 sec Start 155: pyTestThreads 141/190 Test #154: pyTestSGroups .......................... Passed 0.42 sec Start 156: pyTestMultithreadedMolSupplier 142/190 Test #143: substructLibraryTest ................... Passed 3.25 sec Start 157: pyTestPropertyLists 143/190 Test #157: pyTestPropertyLists .................... Passed 0.27 sec Start 158: molStandardizeTest 144/190 Test #156: pyTestMultithreadedMolSupplier ......... Passed 0.43 sec Start 159: molNormalizeTest 145/190 Test #159: molNormalizeTest ....................... Passed 0.14 sec Start 160: molValidateTest 146/190 Test #160: molValidateTest ........................ Passed 0.11 sec Start 161: molChargeTest 147/190 Test #161: molChargeTest .......................... Passed 0.11 sec Start 162: molTautomerTest 148/190 Test #158: molStandardizeTest ..................... Passed 1.22 sec Start 163: molStandardizeSmallTest 149/190 Test #163: molStandardizeSmallTest ................ Passed 0.10 sec Start 164: molFragmentTest 150/190 Test #164: molFragmentTest ........................ Passed 0.08 sec Start 165: molStandardizeCatchTest 151/190 Test #165: molStandardizeCatchTest ................ Passed 0.08 sec Start 166: pyMolStandardize 152/190 Test #155: pyTestThreads .......................... Passed 2.49 sec Start 167: testScaffoldNetwork 153/190 Test #146: pyRGroupDecomposition .................. Passed 5.00 sec Start 168: pyScaffoldNetwork 154/190 Test #145: testRGroupDecomp ....................... Passed 5.57 sec Start 169: pyScaffoldNetworkPickling 155/190 Test #168: pyScaffoldNetwork ...................... Passed 0.31 sec Start 170: testMolEnumerator 156/190 Test #170: testMolEnumerator ...................... Passed 0.08 sec Start 171: pyMolEnumerator 157/190 Test #169: pyScaffoldNetworkPickling .............. Passed 0.33 sec Start 172: testAbbreviations 158/190 Test #172: testAbbreviations ...................... Passed 0.05 sec Start 173: pyAbbreviations 159/190 Test #171: pyMolEnumerator ........................ Passed 0.26 sec Start 174: testQuery 160/190 Test #174: testQuery .............................. Passed 0.02 sec Start 175: testMatCalc 161/190 Test #175: testMatCalc ............................ Passed 0.01 sec Start 176: pyMatCalc 162/190 Test #173: pyAbbreviations ........................ Passed 0.31 sec Start 177: testSimDivPickers 163/190 Test #177: testSimDivPickers ...................... Passed 0.01 sec Start 178: pickersTestsCatch 164/190 Test #167: testScaffoldNetwork .................... Passed 1.21 sec Start 179: pySimDivPickers 165/190 Test #178: pickersTestsCatch ...................... Passed 0.11 sec Start 180: pyRanker 166/190 Test #180: pyRanker ............................... Passed 0.25 sec Start 181: testChemicalFeatures 167/190 Test #181: testChemicalFeatures ................... Passed 0.01 sec Start 182: pyFeatures 168/190 Test #176: pyMatCalc .............................. Passed 0.72 sec Start 183: pythonTestDbCLI 169/190 Test #162: molTautomerTest ........................ Passed 3.18 sec Start 184: pythonTestDirML 170/190 Test #182: pyFeatures ............................. Passed 0.27 sec Start 185: pythonTestDirDataStructs 171/190 Test #166: pyMolStandardize ....................... Passed 2.53 sec Start 186: pythonTestDirDbase 172/190 Test #186: pythonTestDirDbase ..................... Passed 0.64 sec Start 187: pythonTestDirSimDivFilters 173/190 Test #185: pythonTestDirDataStructs ............... Passed 1.16 sec Start 188: pythonTestDirVLib 174/190 Test #179: pySimDivPickers ........................ Passed 1.83 sec Start 189: pythonTestDirChem 175/190 Test #187: pythonTestDirSimDivFilters ............. Passed 0.39 sec Start 190: pythonTestSping 176/190 Test #188: pythonTestDirVLib ...................... Passed 0.60 sec 177/190 Test #190: pythonTestSping ........................ Passed 0.68 sec 178/190 Test #144: pySubstructLibrary ..................... Passed 9.09 sec 179/190 Test #23: testMMFFForceField ..................... Passed 21.75 sec 180/190 Test #117: pyMolAlign ............................. Passed 16.32 sec 181/190 Test #137: pyCIPLabelsValidation .................. Passed 12.12 sec 182/190 Test #151: pyGraphMolWrap ......................... Passed 12.21 sec 183/190 Test #27: graphmolTest1 .......................... Passed 27.01 sec 184/190 Test #114: pyDistGeomHelpers ...................... Passed 22.98 sec 185/190 Test #184: pythonTestDirML ........................ Passed 10.60 sec 186/190 Test #5: testConcurrentQueue .................... Passed 31.14 sec 187/190 Test #183: pythonTestDbCLI ........................ Passed 14.04 sec 188/190 Test #116: testO3AAlign ........................... Passed 30.43 sec 189/190 Test #113: testDistGeomHelpers .................... Passed 40.39 sec 190/190 Test #189: pythonTestDirChem ......................***Failed 81.36 sec ...... ---------------------------------------------------------------------- Ran 6 tests in 0.111s OK ...... ---------------------------------------------------------------------- Ran 6 tests in 0.048s OK ....[14:34:54] **** Pre-condition Violation valence not defined for atoms not associated with molecules Violation occurred on line 313 in file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Atom.cpp Failed Expression: dp_mol **** . ---------------------------------------------------------------------- Ran 5 tests in 0.014s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.008s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.010s OK ...................... ---------------------------------------------------------------------- Ran 22 tests in 0.026s OK .....s.................ss ---------------------------------------------------------------------- Ran 25 tests in 0.161s OK (skipped=3) ..s ---------------------------------------------------------------------- Ran 3 tests in 0.136s OK (skipped=1) ................................... ---------------------------------------------------------------------- Ran 35 tests in 1.040s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.023s OK . ---------------------------------------------------------------------- Ran 1 test in 0.012s OK ....... ---------------------------------------------------------------------- Ran 7 tests in 0.041s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.042s OK .ss.ss....... ---------------------------------------------------------------------- Ran 13 tests in 1.067s OK (skipped=4) .........F.......[14:35:26] WARNING: More than one matching pattern found - picking one [14:35:26] WARNING: More than one matching pattern found - picking one .[14:35:26] WARNING: More than one matching pattern found - picking one .. ====================================================================== FAIL: testEnumerateStereoisomersRandomSamplingShouldBeDeterministicAndPortable (__main__.TestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202009.4/rdkit/Chem/UnitTestMol3D.py", line 229, 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 20 tests in 26.991s 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'} ........ ---------------------------------------------------------------------- Ran 8 tests in 0.087s OK ....[14:35:29] WARNING: not removing hydrogen atom without neighbors [14:35:29] WARNING: not removing hydrogen atom without neighbors [14:35:29] WARNING: not removing hydrogen atom without neighbors ......... ---------------------------------------------------------------------- Ran 13 tests in 2.376s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.976s OK ...... ---------------------------------------------------------------------- Ran 6 tests in 0.254s OK ..............s..s........ ---------------------------------------------------------------------- Ran 26 tests in 2.712s OK (skipped=2) ............./build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/rdkit/Chem/BRICS.py:291: DeprecationWarning: The *random* parameter to shuffle() has been deprecated since Python 3.9 and will be removed in a subsequent version. random.shuffle(indices, random=random.random) /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/rdkit/Chem/BRICS.py:299: DeprecationWarning: The *random* parameter to shuffle() has been deprecated since Python 3.9 and will be removed in a subsequent version. random.shuffle(compats, random=random.random) .[14:35:42] WARNING: More than one matching pattern found - picking one [14:35:42] WARNING: More than one matching pattern found - picking one ........... ---------------------------------------------------------------------- Ran 25 tests in 7.639s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.039s OK ..s... ---------------------------------------------------------------------- Ran 6 tests in 0.586s OK (skipped=1) .[14:35:44] WARNING: not removing hydrogen atom without neighbors .[14:35:44] WARNING: not removing hydrogen atom without neighbors .[14:35:44] WARNING: no name column found on line 1 [14:35:44] WARNING: no name column found on line 2 [14:35:44] WARNING: no name column found on line 3 [14:35:44] WARNING: no name column found on line 4 [14:35:44] WARNING: no name column found on line 5 [14:35:44] WARNING: no name column found on line 6 [14:35:44] WARNING: no name column found on line 7 [14:35:44] WARNING: no name column found on line 8 [14:35:44] WARNING: no name column found on line 9 [14:35:44] WARNING: no name column found on line 10 [14:35:44] WARNING: no name column found on line 11 [14:35:44] WARNING: no name column found on line 12 [14:35:44] WARNING: no name column found on line 13 [14:35:44] WARNING: no name column found on line 14 [14:35:44] WARNING: no name column found on line 15 [14:35:44] WARNING: no name column found on line 16 [14:35:44] WARNING: no name column found on line 17 [14:35:44] WARNING: no name column found on line 18 [14:35:44] WARNING: no name column found on line 19 [14:35:44] WARNING: no name column found on line 20 [14:35:44] WARNING: no name column found on line 21 [14:35:44] WARNING: no name column found on line 22 [14:35:44] WARNING: no name column found on line 23 [14:35:44] WARNING: no name column found on line 24 [14:35:44] WARNING: no name column found on line 25 [14:35:44] WARNING: no name column found on line 26 [14:35:44] WARNING: no name column found on line 27 [14:35:44] WARNING: no name column found on line 28 [14:35:44] WARNING: no name column found on line 29 [14:35:44] WARNING: no name column found on line 30 [14:35:44] WARNING: no name column found on line 31 [14:35:44] WARNING: no name column found on line 32 [14:35:44] WARNING: no name column found on line 33 [14:35:44] WARNING: no name column found on line 34 [14:35:44] WARNING: no name column found on line 35 [14:35:44] WARNING: no name column found 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found on line 188 [14:35:44] WARNING: no name column found on line 189 [14:35:44] WARNING: no name column found on line 190 [14:35:44] WARNING: no name column found on line 191 [14:35:44] WARNING: no name column found on line 192 [14:35:44] WARNING: no name column found on line 193 [14:35:44] WARNING: no name column found on line 194 [14:35:44] WARNING: no name column found on line 195 [14:35:44] WARNING: no name column found on line 196 [14:35:44] WARNING: no name column found on line 197 [14:35:44] WARNING: no name column found on line 198 [14:35:44] WARNING: no name column found on line 199 [14:35:44] WARNING: no name column found on line 200 [14:35:44] WARNING: no name column found on line 201 [14:35:44] WARNING: no name column found on line 202 [14:35:44] WARNING: no name column found on line 203 [14:35:44] WARNING: no name column found on line 204 [14:35:44] WARNING: no name column found on line 205 [14:35:44] WARNING: no name column found on line 206 [14:35:44] WARNING: no name column found on line 207 [14:35:44] WARNING: no name column found on line 208 [14:35:44] WARNING: no name column found on line 209 [14:35:44] WARNING: no name column found on line 210 [14:35:44] WARNING: no name column found on line 211 [14:35:44] WARNING: no name column found on line 212 [14:35:44] WARNING: no name column found on line 213 [14:35:44] WARNING: no name column found on line 214 [14:35:44] WARNING: no name column found on line 215 [14:35:44] WARNING: no name column found on line 216 ...... ---------------------------------------------------------------------- Ran 9 tests in 0.094s OK .................. ---------------------------------------------------------------------- Ran 18 tests in 0.617s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.075s OK ........ ---------------------------------------------------------------------- Ran 8 tests in 0.024s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.014s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.012s OK . ---------------------------------------------------------------------- Ran 1 test in 0.074s OK ........ ---------------------------------------------------------------------- Ran 8 tests in 0.001s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.003s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.001s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.003s OK ....... ---------------------------------------------------------------------- Ran 7 tests in 0.013s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.015s OK .... ---------------------------------------------------------------------- Ran 4 tests in 2.031s OK .......... ---------------------------------------------------------------------- Ran 10 tests in 0.035s OK . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK .......... ---------------------------------------------------------------------- Ran 10 tests in 0.003s OK ..../build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/rdkit/Chem/Randomize.py:29: DeprecationWarning: The *random* parameter to shuffle() has been deprecated since Python 3.9 and will be removed in a subsequent version. random.shuffle(order, random=random.random) . ---------------------------------------------------------------------- Ran 5 tests in 0.053s OK ..................... ---------------------------------------------------------------------- Ran 21 tests in 4.750s OK mol_197 218.97,36.12,110.98,11.56,110.32,11.04,95.23,10.25,0.00 mol_223 252.10,7.34,135.48,1.38,135.41,1.39,85.51,0.37,0.00 mol_269 216.26,5.82,105.00,0.87,103.81,0.89,89.27,0.92,6.00 . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK ...[14:35:56] **** Pre-condition Violation molecule has no conformers Violation occurred on line 37 in file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp Failed Expression: dp_mol->getNumConformers() **** . ---------------------------------------------------------------------- Ran 4 tests in 0.015s OK .. ---------------------------------------------------------------------- Ran 2 tests in 14.242s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.084s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.009s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.016s OK .....[14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors [14:36:12] WARNING: not removing hydrogen atom without neighbors ..... ---------------------------------------------------------------------- Ran 10 tests in 0.271s OK ssssss......s..... ---------------------------------------------------------------------- Ran 18 tests in 0.210s OK (skipped=7) s ---------------------------------------------------------------------- Ran 1 test in 0.000s OK (skipped=1) .......... ---------------------------------------------------------------------- Ran 10 tests in 0.503s OK ..[14:36:14] SMARTS Parse Error: syntax error while parsing: boromicacid [14:36:14] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' [14:36:14] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide [14:36:14] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' [14:36:14] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride [14:36:14] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' [14:36:14] reaction has no reactants [14:36:14] reaction has no products [14:36:14] initialization failed [14:36:14] reaction has no reactants [14:36:14] reaction has no products . ---------------------------------------------------------------------- Ran 3 tests in 0.021s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.010s OK !!! TEST FAILURE: python UnitTestMol3D.py {} 99% tests passed, 2 tests failed out of 190 Total Test time (real) = 102.37 sec The following tests FAILED: 128 - testFMCS (Child aborted) 189 - pythonTestDirChem (Failed) Errors while running CTest make[2]: *** [Makefile:128: test] Error 8 make[2]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' dh_auto_test: error: cd obj-i686-linux-gnu && make -j15 test ARGS\+=-j15 returned exit code 2 make[1]: [debian/rules:126: override_dh_auto_test] Error 25 (ignored) make[1]: Leaving directory '/build/reproducible-path/rdkit-202009.4' fakeroot debian/rules binary dh binary --with python3 --buildsystem=cmake --parallel dh: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_testroot -O--buildsystem=cmake -O--parallel dh_prep -O--buildsystem=cmake -O--parallel dh_installdirs -O--buildsystem=cmake -O--parallel dh_installdirs: warning: Compatibility levels before 10 are deprecated (level 9 in use) debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rdkit-202009.4' dh_auto_install dh_auto_install: warning: Compatibility levels before 10 are deprecated (level 9 in use) cd obj-i686-linux-gnu && make -j15 install DESTDIR=/build/reproducible-path/rdkit-202009.4/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202009.4 -B/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f External/catch/CMakeFiles/catch.dir/build.make 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make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/INCHI-API /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu 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make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/RDGeneral/CMakeFiles/RDGeneral.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 0%] Built target RDStreams [ 0%] Built target hc [ 1%] Built target RDGeneral make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/EigenSolvers 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cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f 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Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && 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make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/DataStructs/CMakeFiles/testFPB.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 6%] Built target rdBase make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/DataStructs/CMakeFiles/testDataStructs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/DataStructs/CMakeFiles/testMultiFPB.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 6%] Built target testFPB make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/Geometry/CMakeFiles/RDGeometryLib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 7%] Built target testDataStructs [ 7%] Built target testMultiFPB make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build [ 7%] Built target testSimDivPickers make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build [ 7%] Built target InfoTheory make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend [ 7%] Built target pickersTestsCatch make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend [ 8%] Built target RDGeometryLib make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ML/Data /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/Data /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --color= make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend [ 8%] Built target Clustering make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 8%] Built target rdMetricMatrixCalc make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make 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Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 8%] Built target Alignment [ 8%] Built target testGrid make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build [ 8%] Built target testTransforms make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build [ 9%] Built target testConrec [ 9%] Built target ChemicalFeatures [ 11%] Built target rdSimDivPickers [ 12%] Built target cDataStructs make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend [ 13%] Built target rdGeometry make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures 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Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/GraphMol.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 13%] Built target cQuantize [ 13%] Built target rdInfoTheory [ 13%] Built target testAlignment [ 17%] Built target GraphMol make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend [ 17%] Built target testChemicalFeatures make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake --color= make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend [ 17%] Built target rdAlignment make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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 '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' 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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 17%] Built target Trajectory make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend 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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 18%] Built target PartialCharges make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend [ 18%] Built target SubstructMatch make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake --color= [ 18%] Built target Subgraphs make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 18%] Built target MolInterchange make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 19%] Built target SmilesParse make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend [ 19%] Built target rdChemicalFeatures make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend [ 20%] Built target MolCatalog make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build [ 21%] Built target rdqueries 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake --color= [ 21%] Built target SLNParse make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake --color= make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 21%] Built target Optimizer make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= [ 21%] Built target rdtrajectory make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend [ 24%] Built target CIPLabeler make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build [ 24%] Built target rdPartialCharges make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend [ 24%] Built target rdMolInterchange make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/test-valgrind.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 24%] Built target graphmolIterTest [ 24%] Built target graphmolqueryTest make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend [ 25%] Built target smiTest2 make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend [ 25%] Built target graphmolcpTest make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend [ 25%] Built target test-valgrind make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend [ 25%] Built target graphmolMemTest1 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake --color= [ 25%] Built target smaTest1 make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake --color= make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend [ 25%] Built target ChemTransforms make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build [ 25%] Built target testSubgraphs1 make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend [ 26%] Built target testSubgraphs2 make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build [ 28%] Built target Fingerprints make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build [ 29%] Built target FilterCatalog make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake --color= [ 29%] Built target testPartialCharges make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend [ 29%] Built target MolTransforms make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 30%] Built target FragCatalog 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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 30%] Built target ReducedGraphs make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend [ 31%] Built target testOptimizer 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake --color= [ 31%] Built target rdCIPLabeler make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend [ 32%] Built target rdSLNParse [ 32%] Built target testSLNParse 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers 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--color= [ 32%] Built target rdMolCatalog [ 32%] Built target MolChemicalFeatures make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= [ 32%] Built target Abbreviations make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 32%] Built target rdMHFPFingerprint 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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 35%] Built target testCIPLabeler make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 36%] Built target rdFingerprintGenerator make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/ForceField/CMakeFiles/ForceField.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build [ 37%] Built target rdfiltercatalog make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 38%] Built target testReducedGraphs make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to 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[ 41%] Built target ForceField make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake --color= [ 42%] Built target rdMolChemicalFeatures make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build [ 44%] Built target SubstructLibrary [ 44%] Built target rdAbbreviations 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build [ 44%] Built target rdReducedGraphs [ 46%] Built target rdchem make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 46%] Built target MolAlign make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend [ 47%] Built target ForceFieldHelpers make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend [ 47%] Built target ShapeHelpers make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/CoordGen/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/CoordGen/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake --color= [ 47%] Built target rdSubstructLibrary make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake --color= [ 48%] Built target rdMolTransforms make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/DistGeom/CMakeFiles/DistGeometry.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build [ 48%] Built target rdForceField [ 48%] Built target rdForceFieldHelpers [ 49%] Built target DistGeometry make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make -f 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'/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake --color= [ 49%] Built target rdShapeHelpers make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build [ 49%] Built target Depictor make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend [ 49%] Built target O3AAlign make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/DistGeom/CMakeFiles/testDistGeom.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 50%] Built target testDistGeom [ 50%] Built target DistGeomHelpers [ 50%] Built target rdCoordGen make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build [ 51%] Built target DistGeom make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 52%] Built target rdDepictor [ 55%] 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/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu 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make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake --color= make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/MMFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --color= make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake --color= make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/hanoiTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolTest1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 55%] Built target chiralityTestsCatch make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/testSGroup.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 55%] Built target graphmolSGroupCatch make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/molBundleTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 55%] Built target hanoiTest make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake --color= make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend [ 56%] Built target graphmolAdjustQueryCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake --color= [ 57%] Built target graphmolTestsCatch 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 57%] Built target graphmolTest1 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake --color= [ 57%] Built target graphmoltestChirality [ 57%] Built target testSGroup make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend [ 58%] Built target molBundleTest [ 58%] Built target graphmoltestPicklerGlobalSetting make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake --color= [ 59%] Built target graphmoltestPickler make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake --color= 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake --color= [ 60%] 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 61%] Built target resMolSupplierTest make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend [ 62%] Built target cxsmilesTest 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake --color= [ 62%] Built target smiTest1 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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build'. [ 62%] Built target testDepictor make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake --color= [ 62%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend [ 62%] Built target smiTestCatch make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend [ 63%] Built target testPropertyLists make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake --color= 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake --color= [ 64%] Built target testSequence make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend [ 64%] Built target testMolSupplier make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake --color= [ 65%] Built target fileParsersTest1 [ 66%] Built target testMolWriter [ 67%] Built target testGeneralFileReader make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'External/CoordGen/CMakeFiles/testCoordGen.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 67%] Built target testCoordGen make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 68%] Built target testUFFForceField make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake --color= make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake --color= [ 68%] Built target testMMFFForceField make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend [ 68%] Built target testTplParser make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake --color= [ 69%] Built target testExtendedStereoParsing make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 69%] Built target substructTestCatch 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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 69%] Built target chemTransformsTestCatch [ 69%] Built target testMultithreadedMolSupplier make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend [ 69%] Built target testSubstructMatch make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend [ 69%] Built target fileParsersCatchTest 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake --color= [ 69%] Built target testChemTransforms 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build [ 69%] Built target filterCatalogTest 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= [ 69%] Built target rdfragcatalog [ 69%] Built target testFragCatalog make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build [ 69%] Built target fpTestCatch make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend [ 69%] Built target testMHFPFingerprint [ 69%] Built target testFingerprints make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --color= [ 70%] Built target testFingerprintGenerators make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 70%] Built target testMMFFForceFieldHelpersMultiThread make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build [ 71%] Built target testMMFFForceFieldHelpers 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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 71%] Built target testUFFForceFieldHelpers make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend [ 71%] Built target testDistGeomHelpers make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake --color= make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build [ 71%] Built target testFeatures make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/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]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build [ 72%] Built target testMolCatalog make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build [ 72%] Built target MMPA make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend [ 73%] Built target trajectoryTest make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 73%] Built target substructLibraryTest [ 73%] Built target rdDistGeom [ 74%] Built target FMCS make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend [ 75%] Built target molInterchangeTest1 make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake --color= [ 75%] Built target testAbbreviations make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build make[4]: Nothing to be done for 'Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 77%] Built target rdmolfiles make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 77%] Built target testMolTransforms [ 79%] Built target Descriptors make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu 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make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions 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'/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 80%] Built target rdFMCS make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend [ 80%] Built target testFMCS [ 80%] Built target testShapeHelpers make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/DependInfo.cmake --color= make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 80%] Built target FMCStest make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu 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directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build 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make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 82%] Built target testATF 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake --color= [ 82%] Built target testCoulombMat make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make 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Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build [ 83%] Built target testWHIM make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build'. make[4]: Leaving directory 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make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake --color= [ 86%] Built target testRGroupDecomp 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake --color= [ 87%] Built target MolHash make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --color= 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake --color= [ 87%] 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f 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'/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 89%] Built target testMolAlign [ 89%] Built target testO3AAlign [ 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/molStandardizeSmallTest.dir/build.make 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Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake --color= [ 92%] Built target deprotectTest [ 92%] Built target rdDeprotect 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake --color= [ 92%] Built target testMolEnumerator [ 92%] Built target rdMolEnumerator make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build [ 94%] Built target MolDraw2D make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= 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-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build [ 94%] Built target TautomerQuery [ 94%] Built target molValidateTest make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' 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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 94%] Built target molStandardizeSmallTest make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend 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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 94%] Built target molChargeTest make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 94%] Built target molTautomerTest [ 95%] Built target molStandardizeTest make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake --color= [ 95%] Built target molNormalizeTest make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake --color= [ 95%] Built target molFragmentTest make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 95%] Built target molStandardizeCatchTest [ 96%] Built target ScaffoldNetwork make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend 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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build [ 97%] Built target rdMolStandardize make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build [ 97%] Built target moldraw2DRxnTest1 [ 97%] Built target moldraw2DTestCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/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-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 97%] Built target rdTautomerQuery make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' [ 98%] Built target tautomerQueryTestCatch [ 99%] Built target rdMolDraw2D [ 99%] Built target testScaffoldNetwork [ 99%] Built target rdScaffoldNetwork [ 99%] Built target rdmolops [100%] Built target moldraw2DTest1 make[3]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/DistanceGeometry -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/DistanceGeometry/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ForceField -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ForceField/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters/SimilarityPickers.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters/__pycache__ -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Numerics -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Numerics/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Geometry -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Geometry/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/Metric -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/Metric/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesOutput.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SDSupply.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesSupply.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmartsRemover.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/__pycache__ -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/DbMolSupply.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/demo.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Output.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Node.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Supply.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Transform.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/__pycache__ -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Filter.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Avalon -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Avalon/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/six.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/StorageUtils.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbReport.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbModule.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/__pycache__ -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbConnection.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbUtils.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbResultSet.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbInfo.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/stringformat.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt/pidQt4.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt/pidQt.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/ReportLab -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/ReportLab/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/ReportLab/pidReportLab.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/TK -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/TK/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/TK/pidTK.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/pidPyart.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/Fontmapping.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/fontinfo.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/pidPS.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/latin1MetricsCache.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/psmetrics.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pidPIL.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-8.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-18.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/metrics.dat -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-24.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-12.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-18.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-12.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/removemedium.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-10.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-8.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-12.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-14.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-18.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-24.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-14.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-10.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-24.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-14.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-10.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util/HTMLPiddler.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/pid.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches/Imaging-1.1.1.diff -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX -- Installing: 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Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__pycache__/pstests.cpython-39.pyc -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__pycache__/pidtest.cpython-39.pyc -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/RDConfig.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Sheridan.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Torsions.py -- Installing: 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/build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/FingerprintUtils.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader_sa.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader_orig.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Crippen.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/TemplateExpand.py -- 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/build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/TorsionFingerprints.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Descriptors.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/PandasTools.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/validations.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/normalize.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/tautomer.py -- Installing: 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/build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/BuilderUtils.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/SubshapeObjects.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/testCombined.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/__pycache__ -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/SubshapeBuilder.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/SubshapeAligner.py -- Installing: 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Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring/Scoring.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring/__pycache__ -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/CrossValidate.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/ClassificationModel.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/__pycache__ -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/AnalyzeComposite.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT/Risk.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT/__pycache__ -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage/__init__.py -- Installing: 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Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/__pycache__ -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Butina.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Clusters.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ScreenComposite.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/CrossValidate.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/KNNModel.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/KNNRegressionModel.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/KNNClassificationModel.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/__pycache__ -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/DistFunctions.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MLUtils -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MLUtils/VoteImg.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MLUtils/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/files.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MatOps.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/__pycache__ -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/BayesComposite.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/Composite.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/__pycache__ -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/AdjustComposite.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/BitRank.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/entropy.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/__pycache__ -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/BitClusterer.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/TreeUtils.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/CrossValidate.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/DecTree.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/SigTree.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/PruneTree.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/QuantTree.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/Tree.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/__init__.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/BuildQuantTree.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/BuildSigTree.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/__pycache__ -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/ID3.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/Forest.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/randomtest.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/TreeVis.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/EnrichPlot.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/RDRandom.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/TestRunner.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/Crippen.txt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/struchk -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.trn -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/Pains -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/Pains/test_data -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/Pains/test_data/wehi_mols.csv -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/Pains/test_data/run_tests.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/Pains/README.md -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/NCI -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/NCI/first_5K.smi -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/NCI/first_200.tpsa.csv -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/RDData.sqlt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/SmartsLib -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/SmartsLib/patty_rules.txt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/bench2.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/DTDs -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Model.dtd -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/DTDs/validate.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/MolStandardize -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/MolStandardize/fragmentPatterns.txt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/MolStandardize/normalizations.txt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/MolStandardize/tautomerTransforms.in -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/MolStandardize/acid_base_pairs.txt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/MolStandardize/acid_base_pairs2.txt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/Fonts -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/FunctionalGroups.txt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/Salts.txt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/rddata.sql -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/An_overview_of_the_RDKit_jp.rst -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/introduction_jp.rst -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/Makefile -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_Book_jp.rst -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/terminology_jp.rst -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/RDKit_cookbook_jp.rst -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/Supplementary_Text_jp.rst -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/Installation_jp.rst -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/Backwards_incompatible_changes_jp.rst -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/index.rst -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_database_cartridge_jp.rst -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_19.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_55.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_30.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_40.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_34.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_46.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_32.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_50.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_48.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_16.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_8.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_37.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_44.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_22.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_33.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_31.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_54.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_60.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_15.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_20.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_58.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_23.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_61.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_52.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_36.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_49.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_39.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_29.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_53.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_41.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_25.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_5.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_26.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_57.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_35.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_2.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_18.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_6.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_14.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_24.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_13.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_11.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_59.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_27.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_43.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_9.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_45.png -- Installing: 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/build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv -- Installing: 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/build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Geometry/UniformGrid3D.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Geometry/Utils.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Geometry/rdGeometry.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Numerics/Matrix.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Numerics/SquareMatrix.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Numerics/SymmMatrix.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Numerics/Vector.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Numerics/Conrec.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitAlignment.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitAlignment.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitAlignment.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Numerics/Alignment/AlignPoints.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Numerics/rdAlignment.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitEigenSolvers.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitEigenSolvers.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitEigenSolvers.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Numerics/EigenSolvers/PowerEigenSolver.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitOptimizer.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitOptimizer.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitOptimizer.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Numerics/Optimizer/BFGSOpt.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitForceField.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitForceField.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitForceField.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/Contrib.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/ForceField.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleBend.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/UFF/BondStretch.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/UFF/Contribs.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/UFF/DistanceConstraint.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleConstraint.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionConstraint.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/UFF/PositionConstraint.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/UFF/Nonbonded.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/UFF/Params.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/UFF/Inversion.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionAngle.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleBend.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/MMFF/BondStretch.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/MMFF/StretchBend.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/MMFF/OopBend.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionAngle.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/MMFF/Nonbonded.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/MMFF/Contribs.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/MMFF/DistanceConstraint.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleConstraint.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionConstraint.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/MMFF/PositionConstraint.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ForceField/MMFF/Params.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ForceField/rdForceField.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDistGeometry.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDistGeometry.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDistGeometry.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/DistGeom/BoundsMatrix.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/DistGeom/ChiralSet.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/DistGeom/ChiralViolationContrib.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/DistGeom/DistGeomUtils.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/DistGeom/DistViolationContrib.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/DistGeom/FourthDimContrib.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/DistGeom/TriangleSmooth.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/DistanceGeometry/DistGeom.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitCatalogs.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitCatalogs.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitCatalogs.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Catalogs/CatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Catalogs/Catalog.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Catalogs/CatalogParams.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitGraphMol.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitGraphMol.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitGraphMol.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Atom.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/atomic_data.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/AtomIterators.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Bond.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/BondIterators.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Canon.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Chirality.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Conformer.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/details.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/GraphMol.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolOps.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolPickler.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/PeriodicTable.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/QueryAtom.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/QueryBond.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/QueryOps.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/RDKitBase.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/RDKitQueries.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Resonance.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/RingInfo.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Rings.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ROMol.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/RWMol.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SanitException.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SubstanceGroup.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/StereoGroup.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MonomerInfo.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/new_canon.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolBundle.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDepictor.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDepictor.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDepictor.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Depictor/DepictUtils.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Depictor/EmbeddedFrag.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Depictor/RDDepictor.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdDepictor.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSmilesParse.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSmilesParse.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSmilesParse.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/primes.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmartsWrite.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParse.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParseOps.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesWrite.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitFileParsers.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitFileParsers.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitFileParsers.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParsers.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParserUtils.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolFileStereochem.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolSupplier.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolWriters.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceParsers.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceWriters.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/GeneralFileReader.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSDMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/PNGParser.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSubstructMatch.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructUtils.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitChemReactions.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitChemReactions.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitChemReactions.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Reaction.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionParser.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionPickler.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionFingerprints.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionUtils.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionRunner.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/PreprocessRxn.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/SanitizeRxn.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/Enumerate.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateBase.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/CartesianProduct.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSample.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdChemReactions.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitChemTransforms.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitChemTransforms.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitChemTransforms.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/ChemTransforms.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/MolFragmenter.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitTautomerQuery.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/TautomerQuery/TautomerQuery.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdTautomerQuery.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSubgraphs.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSubgraphs.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSubgraphs.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/Subgraphs.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/SubgraphUtils.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitFilterCatalog.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalog.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatcherBase.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatchers.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdfiltercatalog.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitFragCatalog.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitFragCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitFragCatalog.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatGenerator.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatParams.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragFPGenerator.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdfragcatalog.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDescriptors.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDescriptors.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDescriptors.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Crippen.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/BCUT.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Lipinski.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolDescriptors.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolSurf.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/ConnectivityDescriptors.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MQN.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/RegisterDescriptor.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Property.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AUTOCORR2D.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Data3Ddescriptors.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolData3Ddescriptors.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/USRDescriptor.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AtomFeat.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolDescriptors3D.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/EEM.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/PBF.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/PMI.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AUTOCORR3D.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/RDF.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MORSE.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/GETAWAY.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/WHIM.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/CoulombMat.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolDescriptors.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitFingerprints.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitFingerprints.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitFingerprints.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/AtomPairs.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/Fingerprints.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MorganFingerprints.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MACCS.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MHFP.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/FingerprintGenerator.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/AtomPairGenerator.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MorganGenerator.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/RDKitFPGenerator.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/TopologicalTorsionGenerator.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/FingerprintUtil.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdFingerprintGenerator.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMHFPFingerprint.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitPartialCharges.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitPartialCharges.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitPartialCharges.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/PartialCharges/GasteigerCharges.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/PartialCharges/GasteigerParams.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdPartialCharges.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolTransforms.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolTransforms.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolTransforms.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolTransforms/MolTransforms.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolTransforms.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/FFConvenience.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/Builder.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/UFF.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/Builder.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/MMFF.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdForceFieldHelpers.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/Embedder.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdDistGeom.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolAlign.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolAlign.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolAlign.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitO3AAlign.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitO3AAlign.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitO3AAlign.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/AlignMolecules.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/O3AAlignMolecules.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolAlign.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/FeatureParser.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitShapeHelpers.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeEncoder.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeUtils.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdShapeHelpers.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolCatalog.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolCatalog.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalog.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolCatalog.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2D.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2Dwx.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DJS.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DUtils.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/DrawText.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/DrawTextSVG.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/DrawTextJS.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolDraw2D.so -- Up-to-date: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/DrawText.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/DrawTextFT.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/DrawTextFTSVG.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/DrawTextFTJS.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/rdMolDraw2D.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitFMCS.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitFMCS.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitFMCS.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FMCS/FMCS.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/FMCS/Graph.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdFMCS.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolHash.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolHash.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolHash.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolHash/MolHash.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolHash/nmmolhash.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolHash.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMMPA.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMMPA.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMMPA.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MMPA/MMPA.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMMPA.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitCIPLabeler.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/CIPLabeler/CIPLabeler.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdCIPLabeler.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDeprotect.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDeprotect.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitDeprotect.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Deprotect/Deprotect.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdDeprotect.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitReducedGraphs.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ReducedGraphs/ReducedGraphs.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdReducedGraphs.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitTrajectory.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitTrajectory.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitTrajectory.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Snapshot.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Trajectory.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSubstructLibrary.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrary.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/PatternFactory.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdSubstructLibrary.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecomp.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdRGroupDecomposition.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolInterchange.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolInterchange.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolInterchange.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/MolInterchange.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/details.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolInterchange.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSLNParse.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSLNParse.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSLNParse.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNAttribs.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNParse.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNParseOps.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdSLNParse.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdchem.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdmolops.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdqueries.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdmolfiles.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdtrajectory.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolStandardize.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolStandardize.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolStandardize.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/MolStandardize.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Metal.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Normalize.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Validate.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Charge.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Tautomer.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Fragment.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/rdMolStandardize.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolEnumerator.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolEnumerator.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitMolEnumerator.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/MolEnumerator/MolEnumerator.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolEnumerator.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitAbbreviations.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitAbbreviations.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitAbbreviations.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/GraphMol/Abbreviations/Abbreviations.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdAbbreviations.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/AndQuery.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/EqualityQuery.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/GreaterEqualQuery.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/GreaterQuery.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/LessEqualQuery.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/LessQuery.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/NullQueryAlgebra.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/OrQuery.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/Query.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/QueryObjects.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/RangeQuery.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/SetQuery.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Query/XOrQuery.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/Features/Feature.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricFuncs.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricMatrixCalc.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/Metric/rdMetricMatrixCalc.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitSimDivPickers.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/SimDivPickers/DistPicker.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/SimDivPickers/LeaderPicker.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/SimDivPickers/HierarchicalClusterPicker.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/SimDivPickers/MaxMinPicker.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters/rdSimDivPickers.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKithc.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKithc.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKithc.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Clustering.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitInfoTheory.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitInfoTheory.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitInfoTheory.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/rdInfoTheory.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/cQuantize.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1.2020.09.4 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1 -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/libRDKitChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ChemicalFeatures/ChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/include/rdkit/ChemicalFeatures/FreeChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/RDPaths.py make[2]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-i686-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/rdkit-202009.4' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/rdkit-202009.4' ln -sf /usr/share/fonts/truetype/freefont/FreeSans.ttf /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/FreeSans.ttf dh_install -ppython3-rdkit /usr/lib/python3 dh_install: warning: Compatibility levels before 10 are deprecated (level 9 in use) rm -f -rf /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/lib/python3/dist-packages/rdkit/docs/ rm -f -rf /build/reproducible-path/rdkit-202009.4/debian/tmp/usr/share/RDKit/Projects/__pycache__ dh_numpy3 dh_install --list-missing dh_install: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_install: warning: Please use dh_missing --list-missing/--fail-missing instead dh_install: warning: This feature will be removed in compat 12. 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 installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example15.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example16.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example17.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example2.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example3.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example4.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example5.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example6.cpp exists in debian/tmp 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: 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usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.ActFuncs.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.CrossValidate.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.NetNode.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.Network.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.Trainers.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.ML.SLT.Risk.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.ML.SLT.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.ML.Scoring.Scoring.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.ML.Scoring.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.ML.ScreenComposite.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.ML.files.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.ML.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.Numerics.rdAlignment.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.Numerics.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.RDConfig.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.RDLogger.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.RDPaths.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.RDRandom.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.SimDivFilters.SimilarityPickers.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.SimDivFilters.rdSimDivPickers.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.SimDivFilters.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.TestRunner.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.VLib.Filter.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.VLib.Node.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.DbMolSupply.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.DbPickleSupplier.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SDSupply.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmartsMolFilter.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmartsRemover.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmilesDupeFilter.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmilesOutput.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmilesSupply.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.demo.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.VLib.Output.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.VLib.Supply.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.VLib.Transform.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.VLib.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.rdBase.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.six.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.utils.cactvs.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.utils.chemdraw.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.utils.chemdraw_qax.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.utils.chemutils.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.utils.comhack.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.utils.fileutils.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.utils.listutils.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.utils.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/source/rdkit.utils.spiral.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/An_overview_of_the_RDKit_jp.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/Backwards_incompatible_changes_jp.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/Installation_jp.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/Makefile exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/RDKit_cookbook_jp.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/Supplementary_Text_jp.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/The_RDKit_Book_jp.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/The_RDKit_database_cartridge_jp.rst exists in debian/tmp but 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-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-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 (54), librdkit1 (106), postgresql-13-rdkit (0), python3-rdkit (1), rdkit-data (3), 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. mkdir -p /build/reproducible-path/rdkit-202009.4/debian/rdkit-doc/usr/share/doc/rdkit/ cp /build/reproducible-path/rdkit-202009.4/Docs/Book/_build/latex/RDKit.pdf /build/reproducible-path/rdkit-202009.4/debian/rdkit-doc/usr/share/doc/rdkit/ cp -a /build/reproducible-path/rdkit-202009.4/Docs/Book/_build/html /build/reproducible-path/rdkit-202009.4/debian/rdkit-doc/usr/share/doc/rdkit/ pg_buildext install /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit build-%v postgresql-%v-rdkit ### PostgreSQL 13 install ### make[2]: Entering directory '/build/reproducible-path/rdkit-202009.4/build-13' /bin/mkdir -p '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib' /bin/mkdir -p '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/share/postgresql/13/extension' /bin/mkdir -p '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/share/postgresql/13/extension' /usr/bin/install -c -m 755 rdkit.so '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/rdkit.so' /usr/bin/install -c -m 644 /build/reproducible-path/rdkit-202009.4/Code/PgSQL/rdkit/rdkit.control '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/share/postgresql/13/extension/' /usr/bin/install -c -m 644 rdkit--3.8.sql '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/share/postgresql/13/extension/' /bin/mkdir -p '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode/rdkit' /bin/mkdir -p '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/ /usr/bin/install -c -m 644 rdkit_io.bc '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 mol_op.bc '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_op.bc '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 sfp_op.bc '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 rxn_op.bc '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 rdkit_gist.bc '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_gist.bc '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_gin.bc '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 low_gist.bc '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 guc.bc '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 cache.bc '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 adapter.bc '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bitstring.bc '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode'/rdkit/./ cd '/build/reproducible-path/rdkit-202009.4/debian/postgresql-13-rdkit/usr/lib/postgresql/13/lib/bitcode' && /usr/lib/llvm-11/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-202009.4/build-13' ### End 13 install ### ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202009.4/debian/rdkit-doc/usr/share/doc/rdkit//html/cppapi/jquery.js ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202009.4/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/jquery.js ln -sf /usr/share/javascript/underscore/underscore.js /build/reproducible-path/rdkit-202009.4/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/underscore.js make[1]: Leaving directory '/build/reproducible-path/rdkit-202009.4' dh_installdocs -O--buildsystem=cmake -O--parallel dh_installdocs: warning: Compatibility levels before 10 are deprecated (level 9 in use) debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/rdkit-202009.4' dh_installchangelogs ReleaseNotes.md make[1]: Leaving directory '/build/reproducible-path/rdkit-202009.4' debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/rdkit-202009.4' dh_python3 -ppython3-rdkit I: dh_python3 fs:343: renaming rdBase.so to rdBase.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming DistGeom.so to DistGeom.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdForceField.so to rdForceField.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdAlignment.so to rdAlignment.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdGeometry.so to rdGeometry.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdAbbreviations.so to rdAbbreviations.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdCIPLabeler.so to rdCIPLabeler.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdChemReactions.so to rdChemReactions.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdChemicalFeatures.so to rdChemicalFeatures.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdCoordGen.so to rdCoordGen.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdDepictor.so to rdDepictor.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdDeprotect.so to rdDeprotect.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdDistGeom.so to rdDistGeom.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdFMCS.so to rdFMCS.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdFingerprintGenerator.so to rdFingerprintGenerator.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdForceFieldHelpers.so to rdForceFieldHelpers.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdMHFPFingerprint.so to rdMHFPFingerprint.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdMMPA.so to rdMMPA.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdMolAlign.so to rdMolAlign.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdMolCatalog.so to rdMolCatalog.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdMolChemicalFeatures.so to rdMolChemicalFeatures.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdMolDescriptors.so to rdMolDescriptors.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdMolEnumerator.so to rdMolEnumerator.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdMolHash.so to rdMolHash.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdMolInterchange.so to rdMolInterchange.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdMolTransforms.so to rdMolTransforms.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdPartialCharges.so to rdPartialCharges.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdRGroupDecomposition.so to rdRGroupDecomposition.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdReducedGraphs.so to rdReducedGraphs.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdSLNParse.so to rdSLNParse.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdShapeHelpers.so to rdShapeHelpers.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdSubstructLibrary.so to rdSubstructLibrary.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdTautomerQuery.so to rdTautomerQuery.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdchem.so to rdchem.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdfiltercatalog.so to rdfiltercatalog.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdfragcatalog.so to rdfragcatalog.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdmolfiles.so to rdmolfiles.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdmolops.so to rdmolops.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdqueries.so to rdqueries.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdtrajectory.so to rdtrajectory.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdMolStandardize.so to rdMolStandardize.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming cDataStructs.so to cDataStructs.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming cQuantize.so to cQuantize.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming Clustering.so to Clustering.cpython-39-i386-linux-gnu.so I: dh_python3 fs:343: renaming rdInfoTheory.so to rdInfoTheory.cpython-39-i386-linux-gnu.so dh_numpy3 -ppython3-rdkit make[1]: Leaving directory '/build/reproducible-path/rdkit-202009.4' dh_installinit -O--buildsystem=cmake -O--parallel dh_installinit: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_lintian -O--buildsystem=cmake -O--parallel dh_lintian: warning: Compatibility levels before 10 are deprecated (level 9 in use) 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_compress: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_compress: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_compress: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_compress: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_compress: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_compress: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_fixperms -O--buildsystem=cmake -O--parallel dh_missing -O--buildsystem=cmake -O--parallel dh_missing: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_strip -O--buildsystem=cmake -O--parallel dh_strip: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_strip: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_strip: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_strip: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_strip: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_strip: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_makeshlibs -O--buildsystem=cmake -O--parallel dh_makeshlibs: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_shlibdeps -O--buildsystem=cmake -O--parallel dh_shlibdeps: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_shlibdeps: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_shlibdeps: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_shlibdeps: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_shlibdeps: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_shlibdeps: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_installdeb -O--buildsystem=cmake -O--parallel dh_installdeb: warning: Compatibility levels before 10 are deprecated (level 9 in use) 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: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package postgresql-13-rdkit: 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 rdkit-data: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-13-rdkit: 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 rdkit-doc: 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-data' in '../rdkit-data_202009.4-1_all.deb'. dpkg-deb: building package 'librdkit1' in '../librdkit1_202009.4-1_i386.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202009.4-1_all.deb'. dpkg-deb: building package 'postgresql-13-rdkit' in '../postgresql-13-rdkit_202009.4-1_i386.deb'. dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202009.4-1_i386.deb'. dpkg-deb: building package 'librdkit1-dbgsym' in '../librdkit1-dbgsym_202009.4-1_i386.deb'. dpkg-deb: building package 'postgresql-13-rdkit-dbgsym' in '../postgresql-13-rdkit-dbgsym_202009.4-1_i386.deb'. dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202009.4-1_i386.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202009.4-1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../rdkit_202009.4-1_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/110048/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/110048/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/110048 and its subdirectories I: Current time: Tue Feb 11 14:37:54 +14 2025 I: pbuilder-time-stamp: 1739234274