Sat Apr 27 08:50:16 UTC 2024 I: starting to build rdkit/experimental/i386 on jenkins on '2024-04-27 08:50' Sat Apr 27 08:50:16 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_1/25480/console.log Sat Apr 27 08:50:16 UTC 2024 I: Downloading source for experimental/rdkit=202309.3-4~exp1 --2024-04-27 08:50:16-- http://cdn-fastly.deb.debian.org/debian/pool/main/r/rdkit/rdkit_202309.3-4%7eexp1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2910 (2.8K) [text/prs.lines.tag] Saving to: ‘rdkit_202309.3-4~exp1.dsc’ 0K .. 100% 132M=0s 2024-04-27 08:50:16 (132 MB/s) - ‘rdkit_202309.3-4~exp1.dsc’ saved [2910/2910] Sat Apr 27 08:50:16 UTC 2024 I: rdkit_202309.3-4~exp1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rdkit Binary: python3-rdkit, rdkit-doc, rdkit-data, librdkit1t64, librdkit-dev, postgresql-16-rdkit Architecture: any all Version: 202309.3-4~exp1 Maintainer: Debichem Team Uploaders: Michael Banck Homepage: http://www.rdkit.org Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/debichem-team/rdkit Vcs-Git: https://salsa.debian.org/debichem-team/rdkit.git Testsuite: autopkgtest Testsuite-Triggers: dpkg-dev, make Build-Depends: bison, catch2, cmake, debhelper-compat (= 13), dh-python, doxygen, flex, imagemagick, latexmk, libboost-dev, libboost-iostreams-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libcairo2-dev, libcoordgen-dev, libeigen3-dev, libfreetype-dev, libmaeparser-dev, librsvg2-bin, libsqlite3-dev, pandoc, postgresql-server-dev-all, python3-dev, python3-myst-parser, python3-numpy, python3-pandas, python3-pil | python3-imaging, python3-recommonmark, python3-sphinx, python3-sqlalchemy, rapidjson-dev, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended Package-List: librdkit-dev deb libdevel optional arch=any librdkit1t64 deb libs optional arch=any postgresql-16-rdkit deb database optional arch=any python3-rdkit deb python optional arch=any rdkit-data deb science optional arch=all rdkit-doc deb doc optional arch=all Checksums-Sha1: 6441bee2cdbc2a1ee07d32fb6e1422f71b91a6ee 61897848 rdkit_202309.3.orig.tar.xz c2b6e3a2a1f16fe809f6ee00c8b850de2056f1e1 25060 rdkit_202309.3-4~exp1.debian.tar.xz Checksums-Sha256: 59f424979d8f2773337ab99605dea4ab4cadbd6c7fd4598fe263d6c19de7a14c 61897848 rdkit_202309.3.orig.tar.xz f8dad991a047e7e0dba38465005a506de89b8b7f2a94673f36a7180b9b353073 25060 rdkit_202309.3-4~exp1.debian.tar.xz Files: 9414102f1ecf8a2a3f62bf46b95f65a7 61897848 rdkit_202309.3.orig.tar.xz 48f16bba6dd1d5dcecd787fafda121e8 25060 rdkit_202309.3-4~exp1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmYrYLsSHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHYMAP/3WLjX2rsQnR+6ygwRttIqp9oFk6Z3kR FWMpBsUcZgQqQWBmjmJLjVkYAPCYU798NUSNnD7ADnA5msed0JNrMNxUiHcSaQnZ +JT76Atux+GfO6U6F4OILV+sllok5aeF3+ajRnqI7DNV5841vNlGz85BkVnwu08f fR9SOHHrK6MsPgaX1o8xOmpLy/5IFMjTgCe5M80XWwz/0Zcl4AUHybUa1tqlWnp3 uz33yJbCYCWSFEZYN6MZdlc82fFotAssqZNYhN1c/DuBAJurQ+wd/aJbGfpnrXfK HlLEuypCLGrICbkLBlPeQHhw6YQpS6fho/wqhoZ0nnl959gpsV0akQhenTp0ttCN 16EGPHQJZoGge6ieyfNMeC/9EYaAmG05ppOT7EHlmpHYjALIMOvRo2CcZ6LfQaP3 zNcqm5rmcR1qLVml0CbKy0aP9FH4r0zhqxBlxALfpDjPNEiYaQcId5r3BOmQz6Yi WwBX82+CzOBYNWms8WKINF3Y3rwcWGjy+iUNG8+T0MvJrsl7wTINwX5FzNe3rJiK rlhdZc4Aq5cJ6j1whSTCRNkZpivv6pHetuhNkSTuY+kgAvjGWlHhrFeJgY5z6WM8 J4FIMCD23oSnVoCm7J3Rj4quLrOE59p2Reoc0vUgX49qBpF8DJa0q6zeI7WC1gU4 S7cWFbt+Hfn/ =IYBp -----END PGP SIGNATURE----- Sat Apr 27 08:50:16 UTC 2024 I: Checking whether the package is not for us Sat Apr 27 08:50:16 UTC 2024 I: Starting 1st build on remote node ionos2-i386.debian.net. Sat Apr 27 08:50:16 UTC 2024 I: Preparing to do remote build '1' on ionos2-i386.debian.net. Sat Apr 27 09:38:06 UTC 2024 I: Deleting $TMPDIR on ionos2-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Apr 26 20:50:20 -12 2024 I: pbuilder-time-stamp: 1714207820 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-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_202309.3-4~exp1.dsc] I: copying [./rdkit_202309.3.orig.tar.xz] I: copying [./rdkit_202309.3-4~exp1.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Apr 26 08:07:23 2024 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./rdkit_202309.3-4~exp1.dsc: no acceptable signature found dpkg-source: info: extracting rdkit in rdkit-202309.3 dpkg-source: info: unpacking rdkit_202309.3.orig.tar.xz dpkg-source: info: unpacking rdkit_202309.3-4~exp1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying NoDownloads.patch dpkg-source: info: applying postgres_Makefile_fixes.patch dpkg-source: info: applying sphinx_imgconverter.patch dpkg-source: info: applying postgres_alternative_test_outputs.patch dpkg-source: info: applying sphinx_compile_fixes.patch dpkg-source: info: applying extra_float_digits dpkg-source: info: applying pg16 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/8420/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='experimental' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='9cab29c226494313b53c396c17af63a6' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='8420' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.SxyPlXPs/pbuilderrc_SyzB --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.SxyPlXPs/b1 --logfile b1/build.log rdkit_202309.3-4~exp1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos2-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 23 07:33 /bin -> usr/bin I: user script /srv/workspace/pbuilder/8420/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: bison, catch2, cmake, debhelper-compat (= 13), dh-python, doxygen, flex, imagemagick, latexmk, libboost-dev, libboost-iostreams-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libcairo2-dev, libcoordgen-dev, libeigen3-dev, libfreetype-dev, libmaeparser-dev, librsvg2-bin, libsqlite3-dev, pandoc, postgresql-server-dev-all, python3-dev, python3-myst-parser, python3-numpy, python3-pandas, python3-pil | python3-imaging, python3-recommonmark, python3-sphinx, python3-sqlalchemy, rapidjson-dev, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19679 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on bison; however: Package bison is not installed. pbuilder-satisfydepends-dummy depends on catch2; however: Package catch2 is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on flex; however: Package flex is not installed. pbuilder-satisfydepends-dummy depends on imagemagick; however: Package imagemagick is not installed. pbuilder-satisfydepends-dummy depends on latexmk; however: Package latexmk is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-python-dev; however: Package libboost-python-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-regex-dev; however: Package libboost-regex-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-system-dev; however: Package libboost-system-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-thread-dev; however: Package libboost-thread-dev is not installed. pbuilder-satisfydepends-dummy depends on libcairo2-dev; however: Package libcairo2-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 libfreetype-dev; however: Package libfreetype-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-myst-parser; however: Package python3-myst-parser is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-pil | python3-imaging; however: Package python3-pil is not installed. Package python3-imaging is not installed. pbuilder-satisfydepends-dummy depends on python3-recommonmark; however: Package python3-recommonmark is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sqlalchemy; however: Package python3-sqlalchemy is not installed. pbuilder-satisfydepends-dummy depends on rapidjson-dev; however: Package rapidjson-dev is not installed. pbuilder-satisfydepends-dummy depends on tex-gyre; however: Package tex-gyre is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bison{a} bsdextrautils{a} ca-certificates{a} catch2{a} clang-16{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-dejavu-mono{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} libapache-pom-java{a} libarchive-zip-perl{a} libarchive13t64{a} libblas3{a} libblkid-dev{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-date-time1.83-dev{a} libboost-date-time1.83.0{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-python-dev{a} libboost-python1.83-dev{a} libboost-python1.83.0{a} libboost-regex-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-thread-dev{a} libboost-thread1.83-dev{a} libboost-thread1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbsd0{a} libbz2-dev{a} libcairo-gobject2{a} libcairo-script-interpreter2{a} libcairo2{a} libcairo2-dev{a} libclang-common-16-dev{a} libclang-cpp16t64{a} libclang1-16t64{a} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libcoordgen-dev{a} libcoordgen3{a} libcurl4t64{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libeigen3-dev{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi-dev{a} libfftw3-double3{a} libfile-stripnondeterminism-perl{a} libfmt9{a} libfontbox-java{a} libfontconfig-dev{a} libfontconfig1{a} libfontenc1{a} libfreetype-dev{a} libfreetype6{a} libfribidi0{a} libgc1{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgfortran5{a} libglib2.0-0t64{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libice-dev{a} libice6{a} libicu-dev{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm16t64{a} liblqr-1-0{a} libltdl7{a} liblua5.4-0{a} liblzo2-2{a} libmaeparser-dev{a} libmaeparser1{a} libmagic-mgc{a} libmagic1t64{a} libmagickcore-6.q16-7t64{a} libmagickwand-6.q16-7t64{a} libmount-dev{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libobjc-13-dev{a} libobjc4{a} libopenjp2-7{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpdfbox-java{a} libpfm4{a} libpipeline1{a} libpixman-1-0{a} libpixman-1-dev{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libpotrace0{a} libpq-dev{a} libpq5{a} libproc2-0{a} libpsl5t64{a} libptexenc1{a} libpthread-stubs0-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libraqm0{a} libraw23t64{a} libreadline8t64{a} librhash0{a} librsvg2-2{a} librsvg2-bin{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libselinux1-dev{a} libsepol-dev{a} libsharpyuv0{a} libsm-dev{a} libsm6{a} libsqlite3-dev{a} libssh2-1t64{a} libssl-dev{a} libsub-override-perl{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libuv1t64{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx11-dev{a} libxau-dev{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-render0-dev{a} libxcb-shm0{a} libxcb-shm0-dev{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxi6{a} libxml2{a} libxml2-dev{a} libxmu6{a} libxpm4{a} libxrender-dev{a} libxrender1{a} libxt6t64{a} libyaml-0-2{a} libz3-4{a} libz3-dev{a} libzzip-0-13t64{a} llvm-16{a} llvm-16-dev{a} llvm-16-linker-tools{a} llvm-16-runtime{a} llvm-16-tools{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} pandoc{a} pandoc-data{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} postgresql-client-16{a} postgresql-client-common{a} postgresql-common{a} postgresql-server-dev-16{a} postgresql-server-dev-all{a} preview-latex-style{a} procps{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-commonmark{a} python3-dateutil{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-greenlet{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-lib2to3{a} python3-markdown-it{a} python3-markupsafe{a} python3-mdit-py-plugins{a} python3-mdurl{a} python3-minimal{a} python3-myst-parser{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pkg-resources{a} python3-pygments{a} python3-recommonmark{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sqlalchemy{a} python3-tz{a} python3-urllib3{a} python3-yaml{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} rapidjson-dev{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} sphinx-common{a} ssl-cert{a} t1utils{a} tex-common{a} tex-gyre{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} tzdata{a} ucf{a} uuid-dev{a} x11-common{a} x11proto-core-dev{a} x11proto-dev{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: apvlv atril binfmt-support bzip2-doc curl default-jre dvisvgm e2fsprogs evince fonts-texgyre fonts-texgyre-math fonts-urw-base35 ghostscript gv javascript-common krb5-locales libarchive-cpio-perl libclang-rt-16-dev libfile-mimeinfo-perl libfl-dev libgdk-pixbuf2.0-bin libgpm2 libheif-plugin-aomenc libheif-plugin-x265 libjson-xs-perl libldap-common libltdl-dev libmagickcore-6.q16-7-extra libmail-sendmail-perl libnet-dbus-perl libpng-tools librsvg2-common libsasl2-modules libspreadsheet-parseexcel-perl libx11-protocol-perl lmodern logrotate lynx mupdf netpbm okular psmisc publicsuffix python3-bottleneck python3-bs4 python3-html5lib python3-lxml python3-matplotlib python3-numexpr python3-odf python3-olefile python3-openpyxl python3-scipy python3-sqlalchemy-ext python3-tables qpdfview qpdfview-ps-plugin ruby systemd texlive-plain-generic tipa tk viewpdf.app wget x11-utils x11-xserver-utils xdg-user-dirs xpdf zathura-pdf-poppler zathura-ps 0 packages upgraded, 340 newly installed, 0 to remove and 0 not upgraded. Need to get 426 MB of archives. After unpacking 2163 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 flex i386 2.6.4-8.2+b2 [415 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 libfftw3-double3 i386 3.3.10-1+b2 [624 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 libpng16-16t64 i386 1.6.43-5 [286 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 libfreetype6 i386 2.13.2+dfsg-1+b4 [449 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 libsharpyuv0 i386 1.3.2-0.4+b1 [107 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 libdav1d7 i386 1.4.1-1 [330 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 libheif-plugin-dav1d i386 1.17.6-1+b2 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 libde265-0 i386 1.0.15-1+b1 [195 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libheif-plugin-libde265 i386 1.17.6-1+b2 [13.7 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libheif1 i386 1.17.6-1+b2 [299 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-3 [169 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 liblcms2-2 i386 2.14-2+b1 [165 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 libglib2.0-0t64 i386 2.78.4-7 [1522 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 liblqr-1-0 i386 0.4.2-2.1+b1 [31.8 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 libltdl7 i386 2.4.7-7 [395 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 libopenjp2-7 i386 2.5.0-2+b3 [197 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 libraw23t64 i386 0.21.2-2.1 [407 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.20-1 [46.9 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 libwebp7 i386 1.3.2-0.4+b1 [314 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 libtiff6 i386 4.5.1+git230720-4 [338 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 libwebpdemux2 i386 1.3.2-0.4+b1 [108 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 libwebpmux3 i386 1.3.2-0.4+b1 [122 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 libbsd0 i386 0.12.2-1 [134 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.17.0-1 [148 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.7-1 [822 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 imagemagick-6-common all 8:6.9.12.98+dfsg1-5.2 [67.1 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 libmagickcore-6.q16-7t64 i386 8:6.9.12.98+dfsg1-5.2 [1758 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 libmagickwand-6.q16-7t64 i386 8:6.9.12.98+dfsg1-5.2 [298 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 postgresql-client-common all 259 [35.9 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 openssl i386 3.2.1-3 [1364 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 ssl-cert all 1.1.2 [21.1 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 ucf all 3.0043+nmu1 [55.2 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 postgresql-common all 259 [168 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 libpython3.11-minimal i386 3.11.9-1 [817 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 python3.11-minimal i386 3.11.9-1 [1918 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.11.8-1 [26.3 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 tzdata all 2024a-3 [255 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-4 [69.3 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-4 [171 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 libpython3.11-stdlib i386 3.11.9-1 [1795 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 python3.11 i386 3.11.9-1 [602 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.11.8-1 [9336 B] Get: 62 http://deb.debian.org/debian unstable/main i386 python3 i386 3.11.8-1 [27.4 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 sgml-base all 1.31 [15.4 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 libproc2-0 i386 2:4.0.4-4 [65.4 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 procps i386 2:4.0.4-4 [876 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 ca-certificates all 20240203 [158 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3 [42.9 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-3+b1 [1195 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40-7 [97.2 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 man-db i386 2.12.1-1 [1421 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 autoconf all 2.71-3 [332 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 autopoint all 0.21-14 [496 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 bison i386 2:3.8.2+dfsg-1+b1 [1186 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 catch2 i386 3.4.0-1 [606 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 libedit2 i386 3.1-20230828-1 [97.5 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 libz3-4 i386 4.8.12-3.1+b2 [7989 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 libllvm16t64 i386 1:16.0.6-25 [26.9 MB] Get: 85 http://deb.debian.org/debian unstable/main i386 libclang-cpp16t64 i386 1:16.0.6-25 [13.6 MB] Get: 86 http://deb.debian.org/debian unstable/main i386 libgc1 i386 1:8.2.6-1 [245 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libobjc4 i386 14-20240330-1 [45.6 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 libobjc-13-dev i386 13.2.0-23 [165 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 libclang-common-16-dev i386 1:16.0.6-25 [656 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 llvm-16-linker-tools i386 1:16.0.6-25 [1349 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libclang1-16t64 i386 1:16.0.6-25 [7729 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 clang-16 i386 1:16.0.6-25 [117 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 libarchive13t64 i386 3.7.2-2 [387 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.20.1-6+b1 [36.1 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.0-2.4 [20.6 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.20.1-6+b1 [83.2 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] Get: 98 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.20.1-6+b1 [360 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.20.1-6+b1 [145 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-6 [20.5 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-6 [60.6 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 libldap-2.5-0 i386 2.5.17+dfsg-1 [198 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.61.0-1+b1 [84.0 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1 [57.4 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b4 [62.0 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.0-4.1+b2 [225 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 libcurl4t64 i386 8.7.1-3 [477 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 libjsoncpp25 i386 1.9.5-6+b2 [89.2 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 librhash0 i386 1.4.3-3+b1 [143 kB] Get: 110 http://deb.debian.org/debian unstable/main i386 libuv1t64 i386 1.48.0-1.1 [156 kB] Get: 111 http://deb.debian.org/debian unstable/main i386 cmake-data all 3.29.2-2 [2167 kB] Get: 112 http://deb.debian.org/debian unstable/main i386 cmake i386 3.29.2-2 [11.9 MB] Get: 113 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 114 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-7 [517 kB] Get: 115 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 116 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 117 http://deb.debian.org/debian unstable/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 118 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 119 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 120 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] Get: 121 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 122 http://deb.debian.org/debian unstable/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 123 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 124 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 125 http://deb.debian.org/debian unstable/main i386 debhelper all 13.15.3 [901 kB] Get: 126 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 127 http://deb.debian.org/debian unstable/main i386 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 128 http://deb.debian.org/debian unstable/main i386 python3-distutils all 3.12.3-1 [131 kB] Get: 129 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 68.1.2-2 [468 kB] Get: 130 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20240422 [107 kB] Get: 131 http://deb.debian.org/debian unstable/main i386 xml-core all 0.19 [20.1 kB] Get: 132 http://deb.debian.org/debian unstable/main i386 docutils-common all 0.20.1+dfsg-3 [128 kB] Get: 133 http://deb.debian.org/debian unstable/main i386 libfmt9 i386 9.1.0+ds1-2 [119 kB] Get: 134 http://deb.debian.org/debian unstable/main i386 doxygen i386 1.9.8+ds-2+b1 [5106 kB] Get: 135 http://deb.debian.org/debian unstable/main i386 fontconfig i386 2.15.0-1.1 [462 kB] Get: 136 http://deb.debian.org/debian unstable/main i386 fonts-lmodern all 2.005-1 [4540 kB] Get: 137 http://deb.debian.org/debian unstable/main i386 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 138 http://deb.debian.org/debian unstable/main i386 icu-devtools i386 72.1-4+b1 [216 kB] Get: 139 http://deb.debian.org/debian unstable/main i386 imagemagick-6.q16 i386 8:6.9.12.98+dfsg1-5.2 [290 kB] Get: 140 http://deb.debian.org/debian unstable/main i386 imagemagick i386 8:6.9.12.98+dfsg1-5.2 [19.4 kB] Get: 141 http://deb.debian.org/debian unstable/main i386 tex-common all 6.18 [32.5 kB] Get: 142 http://deb.debian.org/debian unstable/main i386 libpaper1 i386 1.1.29 [12.7 kB] Get: 143 http://deb.debian.org/debian unstable/main i386 libpaper-utils i386 1.1.29 [8972 B] Get: 144 http://deb.debian.org/debian unstable/main i386 libkpathsea6 i386 2023.20230311.66589-9+b2 [157 kB] Get: 145 http://deb.debian.org/debian unstable/main i386 libptexenc1 i386 2023.20230311.66589-9+b2 [48.3 kB] Get: 146 http://deb.debian.org/debian unstable/main i386 libsynctex2 i386 2023.20230311.66589-9+b2 [64.9 kB] Get: 147 http://deb.debian.org/debian unstable/main i386 libtexlua53-5 i386 2023.20230311.66589-9+b2 [128 kB] Get: 148 http://deb.debian.org/debian unstable/main i386 t1utils i386 1.41-4 [62.3 kB] Get: 149 http://deb.debian.org/debian unstable/main i386 libpixman-1-0 i386 0.42.2-1+b1 [555 kB] Get: 150 http://deb.debian.org/debian unstable/main i386 libxcb-render0 i386 1.17.0-1 [115 kB] Get: 151 http://deb.debian.org/debian unstable/main i386 libxcb-shm0 i386 1.17.0-1 [105 kB] Get: 152 http://deb.debian.org/debian unstable/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 153 http://deb.debian.org/debian unstable/main i386 libcairo2 i386 1.18.0-3+b1 [588 kB] Get: 154 http://deb.debian.org/debian unstable/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 155 http://deb.debian.org/debian unstable/main i386 libharfbuzz0b i386 8.3.0-2+b1 [2234 kB] Get: 156 http://deb.debian.org/debian unstable/main i386 libpotrace0 i386 1.16-2+b1 [24.2 kB] Get: 157 http://deb.debian.org/debian unstable/main i386 libteckit0 i386 2.5.12+ds1-1 [284 kB] Get: 158 http://deb.debian.org/debian unstable/main i386 x11-common all 1:7.7+23 [252 kB] Get: 159 http://deb.debian.org/debian unstable/main i386 libice6 i386 2:1.0.10-1 [60.8 kB] Get: 160 http://deb.debian.org/debian unstable/main i386 libsm6 i386 2:1.2.3-1 [35.7 kB] Get: 161 http://deb.debian.org/debian unstable/main i386 libxt6t64 i386 1:1.2.1-1.2 [193 kB] Get: 162 http://deb.debian.org/debian unstable/main i386 libxmu6 i386 2:1.1.3-3+b2 [60.5 kB] Get: 163 http://deb.debian.org/debian unstable/main i386 libxpm4 i386 1:3.5.17-1+b1 [57.8 kB] Get: 164 http://deb.debian.org/debian unstable/main i386 libxaw7 i386 2:1.0.14-1+b2 [208 kB] Get: 165 http://deb.debian.org/debian unstable/main i386 libxi6 i386 2:1.8.1-1 [81.0 kB] Get: 166 http://deb.debian.org/debian unstable/main i386 libzzip-0-13t64 i386 0.13.72+dfsg.1-1.2+b1 [58.1 kB] Get: 167 http://deb.debian.org/debian unstable/main i386 texlive-binaries i386 2023.20230311.66589-9+b2 [8273 kB] Get: 168 http://deb.debian.org/debian unstable/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 169 http://deb.debian.org/debian unstable/main i386 texlive-base all 2023.20240207-1 [22.0 MB] Get: 170 http://deb.debian.org/debian unstable/main i386 texlive-latex-base all 2023.20240207-1 [1255 kB] Get: 171 http://deb.debian.org/debian unstable/main i386 latexmk all 1:4.85-1 [501 kB] Get: 172 http://deb.debian.org/debian unstable/main i386 libapache-pom-java all 29-2 [5276 B] Get: 173 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 174 http://deb.debian.org/debian unstable/main i386 uuid-dev i386 2.40-7 [44.4 kB] Get: 175 http://deb.debian.org/debian unstable/main i386 libblkid-dev i386 2.40-7 [224 kB] Get: 176 http://deb.debian.org/debian unstable/main i386 libboost1.83-dev i386 1.83.0-2.1+b1 [10.6 MB] Get: 177 http://deb.debian.org/debian unstable/main i386 libboost-atomic1.83.0 i386 1.83.0-2.1+b1 [234 kB] Get: 178 http://deb.debian.org/debian unstable/main i386 libboost-atomic1.83-dev i386 1.83.0-2.1+b1 [235 kB] Get: 179 http://deb.debian.org/debian unstable/main i386 libboost-chrono1.83.0t64 i386 1.83.0-2.1+b1 [241 kB] Get: 180 http://deb.debian.org/debian unstable/main i386 libboost-chrono1.83-dev i386 1.83.0-2.1+b1 [247 kB] Get: 181 http://deb.debian.org/debian unstable/main i386 libboost-date-time1.83.0 i386 1.83.0-2.1+b1 [230 kB] Get: 182 http://deb.debian.org/debian unstable/main i386 libboost-serialization1.83.0 i386 1.83.0-2.1+b1 [341 kB] Get: 183 http://deb.debian.org/debian unstable/main i386 libboost-serialization1.83-dev i386 1.83.0-2.1+b1 [384 kB] Get: 184 http://deb.debian.org/debian unstable/main i386 libboost-date-time1.83-dev i386 1.83.0-2.1+b1 [239 kB] Get: 185 http://deb.debian.org/debian unstable/main i386 libboost-dev i386 1.83.0.2+b2 [3840 B] Get: 186 http://deb.debian.org/debian unstable/main i386 libboost-regex1.83.0 i386 1.83.0-2.1+b1 [328 kB] Get: 187 http://deb.debian.org/debian unstable/main i386 libicu-dev i386 72.1-4+b1 [10.6 MB] Get: 188 http://deb.debian.org/debian unstable/main i386 libboost-regex1.83-dev i386 1.83.0-2.1+b1 [347 kB] Get: 189 http://deb.debian.org/debian unstable/main i386 libboost-iostreams1.83-dev i386 1.83.0-2.1+b1 [264 kB] Get: 190 http://deb.debian.org/debian unstable/main i386 libboost-iostreams-dev i386 1.83.0.2+b2 [3588 B] Get: 191 http://deb.debian.org/debian unstable/main i386 libboost-python1.83.0 i386 1.83.0-2.1+b1 [358 kB] Get: 192 http://deb.debian.org/debian unstable/main i386 libpython3.11t64 i386 3.11.9-1 [1982 kB] Get: 193 http://deb.debian.org/debian unstable/main i386 libexpat1-dev i386 2.6.2-1 [165 kB] Get: 194 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg-3.1 [915 kB] Get: 195 http://deb.debian.org/debian unstable/main i386 libpython3.11-dev i386 3.11.9-1 [4632 kB] Get: 196 http://deb.debian.org/debian unstable/main i386 libpython3-dev i386 3.11.8-1 [9600 B] Get: 197 http://deb.debian.org/debian unstable/main i386 python3.11-dev i386 3.11.9-1 [501 kB] Get: 198 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 199 http://deb.debian.org/debian unstable/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 200 http://deb.debian.org/debian unstable/main i386 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 201 http://deb.debian.org/debian unstable/main i386 python3-dev i386 3.11.8-1 [26.1 kB] Get: 202 http://deb.debian.org/debian unstable/main i386 libboost-python1.83-dev i386 1.83.0-2.1+b1 [392 kB] Get: 203 http://deb.debian.org/debian unstable/main i386 libboost-python-dev i386 1.83.0.2+b2 [3900 B] Get: 204 http://deb.debian.org/debian unstable/main i386 libboost-regex-dev i386 1.83.0.2+b2 [3872 B] Get: 205 http://deb.debian.org/debian unstable/main i386 libboost-system1.83.0 i386 1.83.0-2.1+b1 [230 kB] Get: 206 http://deb.debian.org/debian unstable/main i386 libboost-system1.83-dev i386 1.83.0-2.1+b1 [231 kB] Get: 207 http://deb.debian.org/debian unstable/main i386 libboost-system-dev i386 1.83.0.2+b2 [3740 B] Get: 208 http://deb.debian.org/debian unstable/main i386 libboost-thread1.83.0 i386 1.83.0-2.1+b1 [270 kB] Get: 209 http://deb.debian.org/debian unstable/main i386 libboost-thread1.83-dev i386 1.83.0-2.1+b1 [279 kB] Get: 210 http://deb.debian.org/debian unstable/main i386 libboost-thread-dev i386 1.83.0.2+b2 [3632 B] Get: 211 http://deb.debian.org/debian unstable/main i386 libbrotli-dev i386 1.1.0-2+b3 [313 kB] Get: 212 http://deb.debian.org/debian unstable/main i386 libbz2-dev i386 1.0.8-5.1 [31.4 kB] Get: 213 http://deb.debian.org/debian unstable/main i386 libcairo-gobject2 i386 1.18.0-3+b1 [129 kB] Get: 214 http://deb.debian.org/debian unstable/main i386 liblzo2-2 i386 2.10-2+b1 [58.0 kB] Get: 215 http://deb.debian.org/debian unstable/main i386 libcairo-script-interpreter2 i386 1.18.0-3+b1 [62.4 kB] Get: 216 http://deb.debian.org/debian unstable/main i386 libpng-dev i386 1.6.43-5 [369 kB] Get: 217 http://deb.debian.org/debian unstable/main i386 libfreetype-dev i386 2.13.2+dfsg-1+b4 [624 kB] Get: 218 http://deb.debian.org/debian unstable/main i386 libpkgconf3 i386 1.8.1-1+b2 [38.5 kB] Get: 219 http://deb.debian.org/debian unstable/main i386 pkgconf-bin i386 1.8.1-1+b2 [30.2 kB] Get: 220 http://deb.debian.org/debian unstable/main i386 pkgconf i386 1.8.1-1+b2 [26.2 kB] Get: 221 http://deb.debian.org/debian unstable/main i386 libfontconfig-dev i386 2.15.0-1.1 [428 kB] Get: 222 http://deb.debian.org/debian unstable/main i386 libffi-dev i386 3.4.6-1 [57.8 kB] Get: 223 http://deb.debian.org/debian unstable/main i386 libglib2.0-data all 2.78.4-7 [1225 kB] Get: 224 http://deb.debian.org/debian unstable/main i386 libglib2.0-bin i386 2.78.4-7 [120 kB] Get: 225 http://deb.debian.org/debian unstable/main i386 python3-packaging all 24.0-1 [45.5 kB] Get: 226 http://deb.debian.org/debian unstable/main i386 libglib2.0-dev-bin i386 2.78.4-7 [159 kB] Get: 227 http://deb.debian.org/debian unstable/main i386 libsepol-dev i386 3.5-2 [384 kB] Get: 228 http://deb.debian.org/debian unstable/main i386 libpcre2-16-0 i386 10.42-4+b1 [244 kB] Get: 229 http://deb.debian.org/debian unstable/main i386 libpcre2-32-0 i386 10.42-4+b1 [233 kB] Get: 230 http://deb.debian.org/debian unstable/main i386 libpcre2-posix3 i386 10.42-4+b1 [55.8 kB] Get: 231 http://deb.debian.org/debian unstable/main i386 libpcre2-dev i386 10.42-4+b1 [759 kB] Get: 232 http://deb.debian.org/debian unstable/main i386 libselinux1-dev i386 3.5-2+b2 [166 kB] Get: 233 http://deb.debian.org/debian unstable/main i386 libmount-dev i386 2.40-7 [25.8 kB] Get: 234 http://deb.debian.org/debian unstable/main i386 libglib2.0-dev i386 2.78.4-7 [1760 kB] Get: 235 http://deb.debian.org/debian unstable/main i386 libpixman-1-dev i386 0.42.2-1+b1 [581 kB] Get: 236 http://deb.debian.org/debian unstable/main i386 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 237 http://deb.debian.org/debian unstable/main i386 x11proto-dev all 2024.1-1 [603 kB] Get: 238 http://deb.debian.org/debian unstable/main i386 x11proto-core-dev all 2024.1-1 [3312 B] Get: 239 http://deb.debian.org/debian unstable/main i386 libice-dev i386 2:1.0.10-1 [70.5 kB] Get: 240 http://deb.debian.org/debian unstable/main i386 libsm-dev i386 2:1.2.3-1 [38.8 kB] Get: 241 http://deb.debian.org/debian unstable/main i386 libxau-dev i386 1:1.0.9-1 [23.3 kB] Get: 242 http://deb.debian.org/debian unstable/main i386 libxdmcp-dev i386 1:1.1.2-3 [42.7 kB] Get: 243 http://deb.debian.org/debian unstable/main i386 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 244 http://deb.debian.org/debian unstable/main i386 libpthread-stubs0-dev i386 0.4-1 [5340 B] Get: 245 http://deb.debian.org/debian unstable/main i386 libxcb1-dev i386 1.17.0-1 [185 kB] Get: 246 http://deb.debian.org/debian unstable/main i386 libx11-dev i386 2:1.8.7-1 [901 kB] Get: 247 http://deb.debian.org/debian unstable/main i386 libxcb-render0-dev i386 1.17.0-1 [119 kB] Get: 248 http://deb.debian.org/debian unstable/main i386 libxcb-shm0-dev i386 1.17.0-1 [107 kB] Get: 249 http://deb.debian.org/debian unstable/main i386 libxext-dev i386 2:1.3.4-1+b1 [110 kB] Get: 250 http://deb.debian.org/debian unstable/main i386 libxrender-dev i386 1:0.9.10-1.1 [42.3 kB] Get: 251 http://deb.debian.org/debian unstable/main i386 libcairo2-dev i386 1.18.0-3+b1 [43.2 kB] Get: 252 http://deb.debian.org/debian unstable/main i386 libcommons-parent-java all 56-1 [10.8 kB] Get: 253 http://deb.debian.org/debian unstable/main i386 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 254 http://deb.debian.org/debian unstable/main i386 libcoordgen3 i386 3.0.2-1+b1 [226 kB] Get: 255 http://deb.debian.org/debian unstable/main i386 libcoordgen-dev i386 3.0.2-1+b1 [46.8 kB] Get: 256 http://deb.debian.org/debian unstable/main i386 libdatrie1 i386 0.2.13-3 [39.5 kB] Get: 257 http://deb.debian.org/debian unstable/main i386 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 258 http://deb.debian.org/debian unstable/main i386 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 259 http://deb.debian.org/debian unstable/main i386 libfontenc1 i386 1:1.1.8-1 [23.1 kB] Get: 260 http://deb.debian.org/debian unstable/main i386 libfribidi0 i386 1.0.13-3+b1 [71.8 kB] Get: 261 http://deb.debian.org/debian unstable/main i386 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get: 262 http://deb.debian.org/debian unstable/main i386 shared-mime-info i386 2.4-4 [760 kB] Get: 263 http://deb.debian.org/debian unstable/main i386 libgdk-pixbuf-2.0-0 i386 2.42.10+dfsg-3+b3 [147 kB] Get: 264 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14-20240330-1 [735 kB] Get: 265 http://deb.debian.org/debian unstable/main i386 libimagequant0 i386 2.18.0-1 [35.6 kB] Get: 266 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 267 http://deb.debian.org/debian unstable/main i386 liblua5.4-0 i386 5.4.6-3+b1 [169 kB] Get: 268 http://deb.debian.org/debian unstable/main i386 libmaeparser1 i386 1.3.1-1+b1 [99.9 kB] Get: 269 http://deb.debian.org/debian unstable/main i386 libmaeparser-dev i386 1.3.1-1+b1 [13.6 kB] Get: 270 http://deb.debian.org/debian unstable/main i386 libncurses6 i386 6.4+20240414-1 [112 kB] Get: 271 http://deb.debian.org/debian unstable/main i386 libncurses-dev i386 6.4+20240414-1 [380 kB] Get: 272 http://deb.debian.org/debian unstable/main i386 libthai-data all 0.1.29-2 [168 kB] Get: 273 http://deb.debian.org/debian unstable/main i386 libthai0 i386 0.1.29-2 [50.1 kB] Get: 274 http://deb.debian.org/debian unstable/main i386 libpango-1.0-0 i386 1.52.1+ds-1 [224 kB] Get: 275 http://deb.debian.org/debian unstable/main i386 libpangoft2-1.0-0 i386 1.52.1+ds-1 [51.1 kB] Get: 276 http://deb.debian.org/debian unstable/main i386 libpangocairo-1.0-0 i386 1.52.1+ds-1 [36.0 kB] Get: 277 http://deb.debian.org/debian unstable/main i386 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 278 http://deb.debian.org/debian unstable/main i386 libpfm4 i386 4.13.0+git32-g0d4ed0e-1 [273 kB] Get: 279 http://deb.debian.org/debian unstable/main i386 libpq5 i386 16.2-2+b1 [225 kB] Get: 280 http://deb.debian.org/debian unstable/main i386 libssl-dev i386 3.2.1-3 [2744 kB] Get: 281 http://deb.debian.org/debian unstable/main i386 libpq-dev i386 16.2-2+b1 [152 kB] Get: 282 http://deb.debian.org/debian unstable/main i386 libraqm0 i386 0.10.1-1+b1 [14.7 kB] Get: 283 http://deb.debian.org/debian unstable/main i386 librsvg2-2 i386 2.58.0+dfsg-1 [2043 kB] Get: 284 http://deb.debian.org/debian unstable/main i386 librsvg2-bin i386 2.58.0+dfsg-1 [2213 kB] Get: 285 http://deb.debian.org/debian unstable/main i386 libsqlite3-dev i386 3.45.3-1 [1173 kB] Get: 286 http://deb.debian.org/debian unstable/main i386 libxml2-dev i386 2.9.14+dfsg-1.3+b2 [849 kB] Get: 287 http://deb.debian.org/debian unstable/main i386 libyaml-0-2 i386 0.2.5-1 [55.9 kB] Get: 288 http://deb.debian.org/debian unstable/main i386 libz3-dev i386 4.8.12-3.1+b2 [90.8 kB] Get: 289 http://deb.debian.org/debian unstable/main i386 llvm-16-runtime i386 1:16.0.6-25 [574 kB] Get: 290 http://deb.debian.org/debian unstable/main i386 llvm-16 i386 1:16.0.6-25 [24.7 MB] Get: 291 http://deb.debian.org/debian unstable/main i386 python3-pygments all 2.17.2+dfsg-1 [818 kB] Get: 292 http://deb.debian.org/debian unstable/main i386 python3-yaml i386 6.0.1-2 [176 kB] Get: 293 http://deb.debian.org/debian unstable/main i386 llvm-16-tools i386 1:16.0.6-25 [510 kB] Get: 294 http://deb.debian.org/debian unstable/main i386 llvm-16-dev i386 1:16.0.6-25 [40.3 MB] Get: 295 http://deb.debian.org/debian unstable/main i386 pandoc-data all 3.1.3-1 [445 kB] Get: 296 http://deb.debian.org/debian unstable/main i386 pandoc i386 3.1.3+ds-3 [35.7 MB] Get: 297 http://deb.debian.org/debian unstable/main i386 postgresql-client-16 i386 16.2-2+b1 [1928 kB] Get: 298 http://deb.debian.org/debian unstable/main i386 postgresql-server-dev-16 i386 16.2-2+b1 [1181 kB] Get: 299 http://deb.debian.org/debian unstable/main i386 postgresql-server-dev-all i386 259 [20.1 kB] Get: 300 http://deb.debian.org/debian unstable/main i386 preview-latex-style all 13.2-1 [350 kB] Get: 301 http://deb.debian.org/debian unstable/main i386 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 302 http://deb.debian.org/debian unstable/main i386 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 303 http://deb.debian.org/debian unstable/main i386 python3-tz all 2024.1-2 [30.9 kB] Get: 304 http://deb.debian.org/debian unstable/main i386 python3-babel all 2.14.0-1 [111 kB] Get: 305 http://deb.debian.org/debian unstable/main i386 python3-certifi all 2023.11.17-1 [155 kB] Get: 306 http://deb.debian.org/debian unstable/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 307 http://deb.debian.org/debian unstable/main i386 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get: 308 http://deb.debian.org/debian unstable/main i386 python3-commonmark all 0.9.1-6 [45.3 kB] Get: 309 http://deb.debian.org/debian unstable/main i386 python3-six all 1.16.0-6 [16.3 kB] Get: 310 http://deb.debian.org/debian unstable/main i386 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 311 http://deb.debian.org/debian unstable/main i386 python3-roman all 3.3-3 [9880 B] Get: 312 http://deb.debian.org/debian unstable/main i386 python3-docutils all 0.20.1+dfsg-3 [389 kB] Get: 313 http://deb.debian.org/debian unstable/main i386 python3-greenlet i386 3.0.1-3 [181 kB] Get: 314 http://deb.debian.org/debian unstable/main i386 python3-idna all 3.6-2 [37.0 kB] Get: 315 http://deb.debian.org/debian unstable/main i386 python3-imagesize all 1.4.1-1 [6688 B] Get: 316 http://deb.debian.org/debian unstable/main i386 python3-markupsafe i386 2.1.5-1 [14.4 kB] Get: 317 http://deb.debian.org/debian unstable/main i386 python3-jinja2 all 3.1.3-1 [119 kB] Get: 318 http://deb.debian.org/debian unstable/main i386 python3-mdurl all 0.1.2-1 [9444 B] Get: 319 http://deb.debian.org/debian unstable/main i386 python3-markdown-it all 3.0.0-2 [62.5 kB] Get: 320 http://deb.debian.org/debian unstable/main i386 python3-mdit-py-plugins all 0.4.0-1 [33.0 kB] Get: 321 http://deb.debian.org/debian unstable/main i386 sphinx-common all 7.2.6-6 [702 kB] Get: 322 http://deb.debian.org/debian unstable/main i386 python3-urllib3 all 1.26.18-2 [116 kB] Get: 323 http://deb.debian.org/debian unstable/main i386 python3-requests all 2.31.0+dfsg-1 [68.6 kB] Get: 324 http://deb.debian.org/debian unstable/main i386 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 325 http://deb.debian.org/debian unstable/main i386 python3-sphinx all 7.2.6-6 [552 kB] Get: 326 http://deb.debian.org/debian unstable/main i386 python3-myst-parser all 3.0.0-1 [77.4 kB] Get: 327 http://deb.debian.org/debian unstable/main i386 python3-numpy i386 1:1.26.4+ds-8 [5469 kB] Get: 328 http://deb.debian.org/debian unstable/main i386 python3-pandas-lib i386 2.1.4+dfsg-7 [7497 kB] Get: 329 http://deb.debian.org/debian unstable/main i386 python3-pandas all 2.1.4+dfsg-7 [3015 kB] Get: 330 http://deb.debian.org/debian unstable/main i386 python3-pil i386 10.3.0-2 [566 kB] Get: 331 http://deb.debian.org/debian unstable/main i386 python3-recommonmark all 0.7.1+ds-5 [17.3 kB] Get: 332 http://deb.debian.org/debian unstable/main i386 python3-sqlalchemy all 1.4.50+ds1-1 [1009 kB] Get: 333 http://deb.debian.org/debian unstable/main i386 rapidjson-dev all 1.1.0+dfsg2-7.2 [97.8 kB] Get: 334 http://deb.debian.org/debian unstable/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 335 http://deb.debian.org/debian unstable/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB] Get: 336 http://deb.debian.org/debian unstable/main i386 tex-gyre all 20180621-6 [6209 kB] Get: 337 http://deb.debian.org/debian unstable/main i386 texlive-fonts-recommended all 2023.20240207-1 [4990 kB] Get: 338 http://deb.debian.org/debian unstable/main i386 texlive-latex-recommended all 2023.20240207-1 [8843 kB] Get: 339 http://deb.debian.org/debian unstable/main i386 texlive-pictures all 2023.20240207-1 [16.7 MB] Get: 340 http://deb.debian.org/debian unstable/main i386 texlive-latex-extra all 2023.20240207-1 [19.7 MB] Fetched 426 MB in 7s (64.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19679 files and directories currently installed.) Preparing to unpack .../00-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package flex. Preparing to unpack .../01-flex_2.6.4-8.2+b2_i386.deb ... Unpacking flex (2.6.4-8.2+b2) ... Selecting previously unselected package libfftw3-double3:i386. Preparing to unpack .../02-libfftw3-double3_3.3.10-1+b2_i386.deb ... Unpacking libfftw3-double3:i386 (3.3.10-1+b2) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../03-libexpat1_2.6.2-1_i386.deb ... Unpacking libexpat1:i386 (2.6.2-1) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../04-libbrotli1_1.1.0-2+b3_i386.deb ... Unpacking libbrotli1:i386 (1.1.0-2+b3) ... Selecting previously unselected package libpng16-16t64:i386. Preparing to unpack .../05-libpng16-16t64_1.6.43-5_i386.deb ... Unpacking libpng16-16t64:i386 (1.6.43-5) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../06-libfreetype6_2.13.2+dfsg-1+b4_i386.deb ... Unpacking libfreetype6:i386 (2.13.2+dfsg-1+b4) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../07-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. 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Processing triggers for libc-bin (2.37-18) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up python3-sphinx (7.2.6-6) ... Setting up python3-myst-parser (3.0.0-1) ... Setting up python3-recommonmark (0.7.1+ds-5) ... Processing triggers for ca-certificates (20240203) ... 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 (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/rdkit-202309.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rdkit_202309.3-4~exp1_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202309.3-4~exp1 dpkg-buildpackage: info: source distribution experimental dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean pg_buildext checkcontrol dh clean --with python3 --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' find /build/reproducible-path/rdkit-202309.3 -name "*.pyc" | xargs rm -f rm -f -r Projects/DbCLI/testData/bzr/ rdkit/Chem/inchi.py rm -f -r Docs/Book/_build Code/docs rdkit/docs Code/doxygen_sqlite3.db rm -f \ Code/ForceField/MMFF/test_data/MMFF94_dative_min.sdf \ Code/ForceField/MMFF/test_data/MMFF94_dative_min_from_SMILES.sdf \ Code/ForceField/MMFF/test_data/MMFF94_hypervalent_min.sdf \ Code/ForceField/MMFF/test_data/MMFF94_hypervalent_min_from_SMILES.sdf \ Code/ForceField/MMFF/test_data/MMFF94_reference.log \ Code/ForceField/MMFF/test_data/MMFF94s_reference.log \ Code/ForceField/MMFF/test_data/testMMFFForceField.log \ Code/GraphMol/Depictor/test_data/cis_trans_cpp.out.sdf \ Code/GraphMol/Depictor/test_data/collisions.out.sdf \ Code/GraphMol/Depictor/test_data/first_200.out.sdf \ Code/GraphMol/Depictor/test_data/test1.out.sdf \ Code/GraphMol/FileParsers/test_data/blah.sdf \ Code/GraphMol/FileParsers/test_data/cdk2_stereo.sdf \ Code/GraphMol/FileParsers/test_data/outNCI_few.sdf \ Code/GraphMol/FileParsers/test_data/outNCI_few.tdt \ Code/GraphMol/FileParsers/test_data/outNCI_first_200.props.sdf \ Code/GraphMol/FileParsers/test_data/outSmiles.csv \ Code/GraphMol/ForceFieldHelpers/UFF/test_data/Issue62.sdf \ Code/GraphMol/MolAlign/test_data/ref_e2_pyCrippenO3A.sdf \ Code/GraphMol/SLNParse/lex.yysln.cpp \ Code/GraphMol/SLNParse/sln.tab.cpp \ Code/GraphMol/SLNParse/sln.tab.hpp \ Code/GraphMol/SmilesParse/lex.yysmarts.cpp \ Code/GraphMol/SmilesParse/lex.yysmiles.cpp \ Code/GraphMol/SmilesParse/smarts.tab.cpp \ Code/GraphMol/SmilesParse/smarts.tab.hpp \ Code/GraphMol/SmilesParse/smiles.tab.cpp \ Code/GraphMol/SmilesParse/smiles.tab.hpp \ Code/GraphMol/Wrap/test_data/outNCI_few.sdf \ Code/GraphMol/Wrap/test_data/outSmiles.txt \ Code/RDGeneral/versions.cpp \ Docs/Book/Cartridge.rst \ Docs/Book/Install.rst \ Docs/Book/Overview.rst \ rdkit/ML/Data/test_data/testgeneral.dat.pkl \ rdkit/ML/Data/test_data/testquant.qdat.pkl rm -f Code/RDGeneral/versions.h rdkit/sping/tests/testallps.ps dh_auto_clean pg_buildext clean /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit build-%v rm -rf build-*/ make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary dh binary --with python3 --buildsystem=cmake dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_auto_configure -- -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=ON -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_THREADSAFE_SSS=ON -DRDK_BUILD_PYTHON_WRAPPERS=ON -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_USE_URF=OFF -DRDK_INSTALL_COMIC_FONTS=OFF -DRDK_BUILD_CAIRO_SUPPORT=ON -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DPYTHON_EXECUTABLE=/usr/bin/python3.11 ../ cd obj-i686-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb 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_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=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 -DRDK_INSTALL_COMIC_FONTS=OFF -DRDK_BUILD_CAIRO_SUPPORT=ON -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DPYTHON_EXECUTABLE=/usr/bin/python3.11 ../ .. -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning (dev) at CMakeLists.txt:293 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python3.11 (found version "3.11.9") CMake Warning (dev) at CMakeLists.txt:302 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonLibs: /usr/lib/i386-linux-gnu/libpython3.11.so (found version "3.11.9") CMake Warning (dev) at Code/cmake/Modules/FindNumPy.cmake:10 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:317 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at Code/cmake/Modules/FindNumPy.cmake:14 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): CMakeLists.txt:317 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning at /usr/share/cmake-3.29/Modules/FindBoost.cmake:2234 (message): No header defined for python-py311; skipping header check (note: header-only libraries have no designated component) Call Stack (most recent call first): CMakeLists.txt:331 (find_package) Python Install directory /usr/lib/python3.11/site-packages PYTHON Py_ENABLE_SHARED: 1 PYTHON USING LINK LINE: -shared -Wl,-O1 -Wl,-Bsymbolic-functions nbval not found, disabling the jupyter tests -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found Boost: /usr/include (found suitable version "1.83.0", minimum required is "1.58.0") found components: system serialization iostreams regex -- Found Boost: /usr/include (found suitable version "1.83.0", minimum required is "1.58.0") found components: system iostreams regex == Using strict rotor definition -- 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 (dev) at Code/GraphMol/FilterCatalog/CMakeLists.txt:5 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Found Cairo: /usr/include/cairo -- Found Freetype: /usr/lib/i386-linux-gnu/libfreetype.so (found version "2.13.2") -- Could NOT find Boost (missing: program_options) (found suitable version "1.83.0", minimum required is "1.58.0") -- Configuring done (3.8s) -- Generating done (1.8s) CMake Warning: Manually-specified variables were not used by the project: CATCH_DIR CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_auto_build cd obj-i686-linux-gnu && make -j11 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202309.3 -B/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/INCHI-API /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake "--color=" make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/depend make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/CoordGen /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake "--color=" make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/RingFamilies /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu 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Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o -MF CMakeFiles/RDGeneral.dir/Invariant.cpp.o.d -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.cpp [ 1%] Built target ringdecomposerlib_support cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o -MF CMakeFiles/hc.dir/hcdriver.c.o.d -o CMakeFiles/hc.dir/hcdriver.c.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/Cluster/Murtagh/hcdriver.c [ 2%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/GA/ga/IntegerStringChromosomePolicy.cpp [ 2%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o -MF CMakeFiles/ga.dir/util/RandomUtil.cpp.o.d -o CMakeFiles/ga.dir/util/RandomUtil.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/GA/util/RandomUtil.cpp [ 2%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/Util.cpp.o -MF CMakeFiles/ga.dir/util/Util.cpp.o.d -o CMakeFiles/ga.dir/util/Util.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/GA/util/Util.cpp [ 2%] Linking CXX shared library ../../lib/libRDKitga.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 [ 2%] Linking CXX static library librdkitCatch.a /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2023.09.3 CMakeFiles/ga.dir/ga/StringChromosome.cpp.o CMakeFiles/ga.dir/ga/Chromosome.cpp.o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/util/RandomUtil.cpp.o CMakeFiles/ga.dir/util/Util.cpp.o /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o -MF CMakeFiles/testMatrices.dir/testMatrices.cpp.o.d -o CMakeFiles/testMatrices.dir/testMatrices.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/testMatrices.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Query && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogParams.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Catalogs/CatalogParams.cpp [ 4%] Linking CXX executable logTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DiscreteDistMat.cpp [ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/HierarchicalClusterPicker.cpp In file included from 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/MultiFPBReader.cpp [ 6%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -MF CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o.d -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/testPickers.cpp [ 6%] Linking CXX executable testRDValue cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDValue.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 6%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o [ 6%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o [ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o [ 6%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -MF CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o.d -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/testDatastructs.cpp [ 9%] Linking CXX executable testSimDivPickers cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/InfoTheory /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 9%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/InfoBitRanker.cpp [ 9%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.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-202309.3/obj-i686-linux-gnu' [ 9%] Built target Clustering [ 9%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp [ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform2D.cpp [ 9%] Linking CXX executable pickersTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSimDivPickers.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKithc.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 9%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2023.09.3 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 9%] Built target InfoTheory [ 9%] Built target pickersTestsCatch 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake "--color=" [ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform3D.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 9%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp [ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/UniformGrid3D.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:15: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*(const double*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here 68 | T res = python::extract(d_seq[which]); | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:19: /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/PickerHelpers.h: In member function 'double pyobjFunctor::operator()(unsigned int, unsigned int)': /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/PickerHelpers.h:52:48: warning: '*(const double*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 52 | return python::extract(dp_obj(i, j)); | ^ /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/PickerHelpers.h:52:48: note: '' declared here 52 | return python::extract(dp_obj(i, j)); | ^ [ 10%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/DiscreteValueVect.cpp [ 10%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 10%] Built target rdMetricMatrixCalc make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ML/Data /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/Data /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 11%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/Data && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcQuantize_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o -MF CMakeFiles/cQuantize.dir/cQuantize.cpp.o.d -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/Data/cQuantize.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp:19: In member function 'double pyobjFunctor::operator()(unsigned int, unsigned int)', inlined from 'unsigned int RDPickers::LeaderPickerState::compact(int*, int*, unsigned int) [with T = pyobjFunctor]' at /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/LeaderPicker.h:263:18: /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/PickerHelpers.h:52:48: warning: '*(const double*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 52 | return python::extract(dp_obj(i, j)); | ^ /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/PickerHelpers.h: In member function 'unsigned int RDPickers::LeaderPickerState::compact(int*, int*, unsigned int) [with T = pyobjFunctor]': /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/PickerHelpers.h:52:48: note: '' declared here 52 | return python::extract(dp_obj(i, j)); | ^ [ 11%] Linking CXX executable testFPB cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp [ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/wrap_SparseBV.cpp [ 13%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 13%] 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o -MF CMakeFiles/GraphMol.dir/Atom.cpp.o.d -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.cpp [ 13%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -MF CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/Wrap/RDBase.cpp:14: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 420 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ [ 13%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 13%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -MF CMakeFiles/Alignment.dir/AlignPoints.cpp.o.d -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/AlignPoints.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 13%] Built target cQuantize make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Geometry /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 14%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o -MF CMakeFiles/testTransforms.dir/testTransforms.cpp.o.d -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/testTransforms.cpp /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:190:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = int]' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:219:26: required from here /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:77:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 77 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:77:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 77 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTanimoto(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:200:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = int]' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:219:26: required from here /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:90:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 90 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:90:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 90 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTversky(const T&, boost::python::list, double, double, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:211:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = int]' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:219:26: required from here /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:104:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 104 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:104:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:190:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long long int]' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:220:28: required from here /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:77:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 77 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:77:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 77 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTanimoto(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:200:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long long int]' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:220:28: required from here /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:90:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 90 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:90:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 90 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTversky(const T&, boost::python::list, double, double, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:211:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long long int]' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:220:28: required from here /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:104:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 104 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:104:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:190:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = unsigned int]' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:221:27: required from here /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:77:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 77 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:77:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 77 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTanimoto(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:200:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = unsigned int]' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:221:27: required from here /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:90:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 90 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:90:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 90 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTversky(const T&, boost::python::list, double, double, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:211:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = unsigned int]' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:221:27: required from here /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:104:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 104 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:104:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:190:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long long unsigned int]' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:222:29: required from here /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:77:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 77 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:77:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 77 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTanimoto(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:200:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long long unsigned int]' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:222:29: required from here /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:90:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 90 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:90:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 90 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTversky(const T&, boost::python::list, double, double, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:211:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long long unsigned int]' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:222:29: required from here /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:104:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 104 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:104:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ [ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp [ 14%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKithc.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 14%] Built target rdSimDivPickers make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Geometry /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o -MF CMakeFiles/testGrid.dir/testGrid.cpp.o.d -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/testGrid.cpp [ 15%] Linking CXX executable testDataStructs cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 15%] Built target testDataStructs make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Geometry /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 15%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/catch_tests.cpp 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 15%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -MF CMakeFiles/rdGeometry.dir/Point.cpp.o.d -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/Point.cpp [ 15%] Linking CXX shared library ../../../lib/libRDKitAlignment.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so make[4]: Leaving directory 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/wrap_FPB.cpp [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/wrap_Utils.cpp [ 17%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2023.09.3 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 17%] Built target ChemicalFeatures make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make 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Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 17%] Built target testConrec [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -MF CMakeFiles/GraphMol.dir/QueryBond.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryBond.cpp [ 17%] Linking CXX executable testAlignment cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E 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make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 17%] Built target testAlignment [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -MF CMakeFiles/GraphMol.dir/Bond.cpp.o.d -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Bond.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:18: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = long long int]': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here 68 | T res = python::extract(d_seq[which]); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = long long unsigned int]': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*(const long long unsigned int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here 68 | T res = python::extract(d_seq[which]); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -MF CMakeFiles/GraphMol.dir/MolOps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:16: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*(const double*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here 68 | T res = python::extract(d_seq[which]); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 18%] Linking CXX executable testChemicalFeatures cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 18%] Built target testChemicalFeatures [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -MF CMakeFiles/GraphMol.dir/FindRings.cpp.o.d -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindRings.cpp [ 18%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 18%] Built target rdAlignment [ 18%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/UniformGrid3D.cpp [ 18%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -MF CMakeFiles/GraphMol.dir/RWMol.cpp.o.d -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -MF CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o.d -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -MF CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/atomic_data.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -MF CMakeFiles/GraphMol.dir/QueryOps.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.cpp [ 18%] Linking CXX shared module ../../../rdkit/rdBase.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -MF CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Canon.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -MF CMakeFiles/GraphMol.dir/AtomIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/AtomIterators.cpp [ 19%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd 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../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o -MF CMakeFiles/GraphMol.dir/Kekulize.cpp.o.d -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Kekulize.cpp [ 19%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -MF CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o.d -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ConjugHybrid.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o -MF CMakeFiles/GraphMol.dir/AddHs.cpp.o.d -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/AddHs.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o -MF CMakeFiles/GraphMol.dir/Matrices.cpp.o.d -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Matrices.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o -MF CMakeFiles/GraphMol.dir/Chirality.cpp.o.d -o CMakeFiles/GraphMol.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o -MF CMakeFiles/GraphMol.dir/RingInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RingInfo.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o -MF CMakeFiles/GraphMol.dir/Conformer.cpp.o.d -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.cpp /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Kekulize.cpp: In function 'void RDKit::{anonymous}::markDbondCands(RDKit::RWMol&, const RDKit::INT_VECT&, boost::dynamic_bitset<>&, RDKit::INT_VECT&, RDKit::INT_VECT&)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Kekulize.cpp:147:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 147 | numNonCandRings < numAtomRings) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o -MF CMakeFiles/GraphMol.dir/Renumber.cpp.o.d -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Renumber.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -MF CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o.d -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/AdjustQuery.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o -MF CMakeFiles/GraphMol.dir/Resonance.cpp.o.d -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Resonance.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -MF CMakeFiles/GraphMol.dir/StereoGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StereoGroup.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o -MF CMakeFiles/GraphMol.dir/new_canon.cpp.o.d -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/new_canon.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -MF CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstanceGroup.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o -MF CMakeFiles/GraphMol.dir/FindStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/FindStereo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindStereo.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -MF CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MonomerInfo.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -MF CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/NontetrahedralStereo.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -MF CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o.d -o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/WedgeBonds.cpp [ 21%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/Matrices.cpp.o CMakeFiles/GraphMol.dir/Chirality.cpp.o CMakeFiles/GraphMol.dir/RingInfo.cpp.o CMakeFiles/GraphMol.dir/Conformer.cpp.o CMakeFiles/GraphMol.dir/Renumber.cpp.o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o CMakeFiles/GraphMol.dir/Resonance.cpp.o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o CMakeFiles/GraphMol.dir/new_canon.cpp.o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o CMakeFiles/GraphMol.dir/FindStereo.cpp.o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1 ../../lib/libRDKitGraphMol.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 21%] Built target GraphMol make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/depend make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend 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 -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParse.cpp [ 21%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -MF CMakeFiles/Trajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.cpp [ 21%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/c++ 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External 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Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o -MF CMakeFiles/MolInterchange.dir/Parser.cpp.o.d -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Parser.cpp [ 21%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -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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/usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 21%] Built target Trajectory 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/GasteigerParams.cpp [ 22%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalogParams.cpp [ 22%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -MF CMakeFiles/rdqueries.dir/Queries.cpp.o.d -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Queries.cpp [ 22%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -MF CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o.d -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/SubgraphUtils.cpp [ 22%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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/usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2023.09.3 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 22%] Built target MolCatalog make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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-202309.3/obj-i686-linux-gnu' [ 22%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -MF CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o.d -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.cpp [ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o cd 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Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParseOps.cpp [ 22%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 23%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -MF CMakeFiles/Optimizer.dir/LinearSearch.cpp.o.d -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/LinearSearch.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 23%] Built target MolTransforms make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -MF CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o.d -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp [ 23%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 23%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 23%] Built target PartialCharges make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[4]: Entering directory 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/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT 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-DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/CIPLabeler.dir/Mancude.cpp.o.d -o 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp [ 24%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -MF CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNAttribs.cpp [ 24%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -MF CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o.d -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp [ 24%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -MF CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o.d -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp [ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/CIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Digraph.cpp [ 27%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o -MF CMakeFiles/MolInterchange.dir/Writer.cpp.o.d -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Writer.cpp [ 27%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 27%] Built target rdPartialCharges 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake "--color=" [ 27%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 27%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 27%] Built target rdChemicalFeatures make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend [ 28%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 28%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o cd 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Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -MF CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o.d -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/testOptimizer.cpp [ 28%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o -MF CMakeFiles/SLNParse.dir/sln.tab.cpp.o.d -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/sln.tab.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 28%] Built target rdqueries make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ForceField /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -MF CMakeFiles/ForceField.dir/ForceField.cpp.o.d -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.cpp [ 28%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rdTrajectory.cpp [ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.cpp [ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o -MF CMakeFiles/CIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Node.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 28%] Built target rdMolCatalog [ 28%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructUtils.cpp [ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmartsWrite.cpp [ 28%] Linking CXX executable testOptimizer cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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-c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Edge.cpp [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Inversion.cpp [ 29%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -MF CMakeFiles/SLNParse.dir/lex.yysln.cpp.o.d -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/lex.yysln.cpp [ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/TorsionAngle.cpp [ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/CIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Sort.cpp [ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/DistanceConstraint.cpp [ 29%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 [ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2023.09.3 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2023.09.3 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 29%] Built target ShapeHelpers make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 29%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/smarts.tab.cpp [ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleConstraint.cpp [ 29%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o 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Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/smiles.tab.cpp [ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/TorsionConstraint.cpp [ 30%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 30%] Built target MolInterchange make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/lex.yysmarts.cpp [ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/PositionConstraint.cpp [ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp [ 31%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2023.09.3 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 31%] Built target SLNParse [ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -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-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Params.cpp [ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD 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Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/BondStretch.cpp [ 31%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/lex.yysmiles.cpp [ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp [ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/StretchBend.cpp [ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp [ 32%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp [ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/OopBend.cpp [ 32%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp [ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionAngle.cpp [ 32%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp [ 32%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp [ 32%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp [ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 32%] Built target rdShapeHelpers 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 32%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -MF CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o.d -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp [ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 33%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -MF 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp [ 33%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule6.cpp [ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Nonbonded.cpp [ 33%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp [ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleConstraint.cpp [ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionConstraint.cpp [ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/PositionConstraint.cpp [ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Params.cpp [ 34%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 34%] Built target SmilesParse make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend make[4]: Entering directory 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -MF CMakeFiles/graphmolcpTest.dir/cptest.cpp.o.d -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/cptest.cpp [ 36%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 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../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 36%] Built target moliteratorTestsCatch make -f 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o -MF CMakeFiles/FilterCatalog.dir/Filters.cpp.o.d -o CMakeFiles/FilterCatalog.dir/Filters.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Filters.cpp [ 36%] Linking CXX executable graphmolcpTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script 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-ldl [ 36%] Linking CXX executable graphmolMemTest1 cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 36%] Linking CXX executable test-valgrind cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-valgrind.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 36%] Built target graphmolcpTest make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend [ 36%] Built target graphmolMemTest1 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-202309.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Fingerprints.cpp [ 36%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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/usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 36%] Built target queryTestsCatch make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/DependInfo.cmake "--color=" [ 36%] Linking CXX executable graphmolIterTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 37%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o.d -o 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp [ 37%] Linking CXX executable smiTest2 cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest2.dir/link.txt --verbose=1 /usr/bin/c++ -g 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o -MF CMakeFiles/testPartialCharges.dir/test1.cpp.o.d -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/test1.cpp [ 37%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalog.cpp [ 38%] Linking CXX executable molbundleTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molbundleTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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/usr/lib/libCatch2.a ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 40%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp [ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o -MF CMakeFiles/Depictor.dir/RDDepictor.cpp.o.d -o CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp [ 41%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security 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External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/CoordGen/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCoordGen_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -MF CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o.d -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/CoordGen/Wrap/rdCoordGen.cpp [ 41%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp [ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganFingerprints.cpp [ 41%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatchers.cpp [ 41%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ 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CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o.d -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp [ 41%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -MF CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp [ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairs.cpp [ 42%] Linking CXX executable smaTest1 cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -MF CMakeFiles/Fingerprints.dir/MACCS.cpp.o.d -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MACCS.cpp [ 42%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp [ 42%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2023.09.3 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2023.09.3 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 42%] Built target Abbreviations 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -MF CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o.d -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp [ 42%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -MF CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/test1.cpp [ 42%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -MF CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o.d -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp [ 42%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so cd 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -MF CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o.d -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp [ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MHFP.cpp [ 42%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend make[4]: 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Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp [ 42%] Linking CXX executable testSLNParse cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 [ 43%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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-ldl /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2023.09.3 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 43%] Built target FragCatalog [ 43%] Built target testSLNParse make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend [ 43%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake "--color=" cd 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp [ 43%] Linking CXX executable testReducedGraphs cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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/usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 43%] Built target testReducedGraphs [ 43%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -MF CMakeFiles/Depictor.dir/DepictUtils.cpp.o.d -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/DepictUtils.cpp [ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat 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/usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 44%] Built target rdReducedGraphs [ 44%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o -MF CMakeFiles/Depictor.dir/Templates.cpp.o.d -o CMakeFiles/Depictor.dir/Templates.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Templates.cpp [ 45%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp [ 45%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp [ 45%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp [ 45%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp [ 45%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp [ 45%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD 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Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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../../../lib/libRDKitDepictor.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o CMakeFiles/Depictor.dir/Templates.cpp.o /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 46%] Built target Depictor make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake "--color=" make[4]: Entering directory 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -MF CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o.d -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 46%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp: In function 'boost::python::api::object RDKit::GetAtomMatch(boost::python::api::object, int)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:45:19: warning: redundant move in return statement [-Wredundant-move] 45 | return std::move(res); | ~~~~~~~~~^~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:45:19: note: remove 'std::move' call [ 46%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/MolFragmenter.cpp [ 46%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 46%] Built target rdMolChemicalFeatures [ 46%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o 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/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 46%] Built target ForceFieldHelpers 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake "--color=" [ 47%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ForceField/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build [ 47%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -MF CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/DistGeomUtils.cpp [ 47%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -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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-DrdForceField_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -MF CMakeFiles/rdForceField.dir/ForceField.cpp.o.d -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/Wrap/ForceField.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/DistViolationContrib.cpp [ 47%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DO3AAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -MF CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o.d -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp [ 48%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -MF CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o.d -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 48%] Built target Fingerprints 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 48%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp [ 49%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/ChiralViolationContrib.cpp make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 49%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -MF CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o.d -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp [ 49%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 49%] Built target rdDepictor /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::UFFConfsHelper(ROMol&, int, int, double, bool)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:49:19: warning: redundant move in return statement [-Wredundant-move] 49 | return std::move(pyres); | ~~~~~~~~~^~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:49:19: note: remove 'std::move' call /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::MMFFConfsHelper(ROMol&, int, int, std::string, double, bool)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:66:19: warning: redundant move in return statement [-Wredundant-move] 66 | return std::move(pyres); | ~~~~~~~~~^~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:66:19: note: remove 'std::move' call /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::FFConfsHelper(ROMol&, ForceFields::PyForceField&, int, int)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:86:19: warning: redundant move in return statement [-Wredundant-move] 86 | return std::move(pyres); | ~~~~~~~~~^~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:86:19: note: remove 'std::move' call /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp: In function 'boost::python::api::object RDKit::FingerprintWrapper::getBitPathsHelper(const RDKit::AdditionalOutput&)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:452:19: warning: redundant move in return statement [-Wredundant-move] 452 | return std::move(res); | ~~~~~~~~~^~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:452:19: note: remove 'std::move' call /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp: In function 'boost::python::api::object RDKit::FingerprintWrapper::getBitInfoMapHelper(const RDKit::AdditionalOutput&)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:467:19: warning: redundant move in return statement [-Wredundant-move] 467 | return std::move(res); | ~~~~~~~~~^~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:467:19: note: remove 'std::move' call [ 49%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 49%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 49%] Built target DistGeometry make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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-202309.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 49%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o [ 49%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/testDistGeom.cpp [ 50%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap/DistGeom.cpp [ 50%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 50%] Built target ChemTransforms make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -MF CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o.d -o CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/CDXMLParser.cpp [ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 50%] Built target rdForceFieldHelpers [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -MF CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/Mol2FileParser.cpp [ 50%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2023.09.3 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 50%] Built target O3AAlign [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileParser.cpp [ 51%] Linking CXX executable testDistGeom cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 51%] Built target testDistGeom [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupParsing.cpp [ 51%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl In file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, from /usr/include/boost/python/object/class_metadata.hpp:14, from /usr/include/boost/python/class.hpp:23, from /usr/include/boost/python.hpp:18, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp:11: In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', inlined from 'ValueT boost::python::stl_input_iterator::dereference() const [with ValueT = unsigned int]' at /usr/include/boost/python/stl_iterator.hpp:48:60, inlined from 'static typename Facade::reference boost::iterators::iterator_core_access::dereference(const Facade&) [with Facade = boost::python::stl_input_iterator]' at /usr/include/boost/iterator/iterator_facade.hpp:631:31, inlined from 'boost::iterators::detail::iterator_facade_base::reference boost::iterators::detail::iterator_facade_base::operator*() const [with Derived = boost::python::stl_input_iterator; Value = unsigned int; CategoryOrTraversal = std::input_iterator_tag; Reference = unsigned int; Difference = int]' at /usr/include/boost/iterator/iterator_facade.hpp:737:53, inlined from 'void std::vector<_Tp, _Alloc>::_M_range_initialize(_InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1670:21, inlined from 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:708:23, inlined from 'std::vector RDKit::MHFPWrapper::ListToVector(const boost::python::api::object&) [with T = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp:28:56: /usr/include/boost/python/extract.hpp:185:11: warning: '*(unsigned int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ In file included from /usr/include/boost/python.hpp:66: /usr/include/boost/python/stl_iterator.hpp: In function 'std::vector RDKit::MHFPWrapper::ListToVector(const boost::python::api::object&) [with T = unsigned int]': /usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here 48 | return extract(this->impl_.current().get())(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 51%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 51%] Built target DistGeom [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupWriting.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 51%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp [ 51%] Built target rdForceField [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileStereochem.cpp [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileWriter.cpp [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp [ 52%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SDWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDWriter.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 52%] Built target rdMHFPFingerprint [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp [ 52%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 52%] Built target rdFingerprintGenerator [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SmilesWriter.cpp [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TDTMolSupplier.cpp [ 52%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 52%] Built target DistGeomHelpers [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TDTWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TDTWriter.cpp [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TplFileParser.cpp [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TplFileWriter.cpp [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -MF CMakeFiles/FileParsers.dir/PDBWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/PDBWriter.cpp [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -MF CMakeFiles/FileParsers.dir/CMLWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/CMLWriter.cpp [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/XYZFileParser.cpp [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MaeMolSupplier.cpp [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceParsers.cpp [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o -MF CMakeFiles/FileParsers.dir/SVGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SVGParser.cpp [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp [ 54%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/FileParsers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDWriter.cpp.o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o CMakeFiles/FileParsers.dir/PDBParser.cpp.o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MaeWriter.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/libRDKitChemTransforms.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1 ../../../lib/libRDKitFileParsers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 54%] Built target FileParsers make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make 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../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so [ 55%] Built target testCoordGen make -f Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -MF CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o.d -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_sgroups.cpp [ 57%] Linking CXX executable graphmolOrganometallicsCatch cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolOrganometallicsCatch.dir/link.txt --verbose=1 [ 57%] Linking CXX executable molBundleTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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/usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 57%] Built target molBundleTest make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake "--color=" [ 57%] Built target 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o -MF CMakeFiles/Descriptors.dir/Crippen.cpp.o.d -o CMakeFiles/Descriptors.dir/Crippen.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Crippen.cpp [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -MF CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o.d -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMolSupplier.cpp [ 59%] Linking CXX executable testDepictor cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so [ 59%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 59%] Built target testDepictor 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -MF CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o.d -o CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testGeneralFileReader.cpp [ 59%] Linking CXX executable smiTest1 cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 59%] Built target smiTest1 make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -MF CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o.d -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp [ 60%] Linking CXX executable testGeneralFileReader cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.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-202309.3/obj-i686-linux-gnu' [ 60%] Built target testGeneralFileReader 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -MF CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o.d -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMolWriter.cpp [ 60%] Linking CXX executable testMultithreadedMolSupplier cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.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-202309.3/obj-i686-linux-gnu' [ 60%] Built target testMultithreadedMolSupplier 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolDescriptors.cpp [ 61%] Linking CXX executable testMolSupplier cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.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-202309.3/obj-i686-linux-gnu' [ 61%] Built target testMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -MF CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o.d -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMol2ToMol.cpp [ 62%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -MF CMakeFiles/Descriptors.dir/MolSurf.cpp.o.d -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolSurf.cpp [ 62%] Linking CXX executable smiTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 62%] Built target smiTestCatch 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -MF CMakeFiles/testSequence.dir/testSequence.cpp.o.d -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testSequence.cpp [ 62%] Linking CXX executable testMol2ToMol cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 62%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -MF CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o.d -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp [ 62%] Linking CXX executable testTplParser cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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"--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -MF CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o.d -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/file_parsers_catch.cpp [ 62%] Linking CXX executable testMolWriter cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 62%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -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_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 62%] Built target graphmolTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -MF CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o.d -o CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp [ 62%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Lipinski.cpp [ 62%] Linking CXX executable testExtendedStereoParsing cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 62%] Built target testExtendedStereoParsing make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -MF CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o.d -o CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp [ 62%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp [ 62%] Linking CXX executable XYZFileParserCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 62%] Built target XYZFileParserCatchTest make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -MF CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o.d -o CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/connectTheDots_catch.cpp [ 62%] Linking CXX executable graphmoltestChirality cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 62%] Built target graphmoltestChirality 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 62%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o -MF CMakeFiles/testSubstructMatch.dir/test1.cpp.o.d -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp [ 62%] Linking CXX executable cdxmlParserCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 62%] Built target cdxmlParserCatchTest 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so 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/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 63%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -MF CMakeFiles/Descriptors.dir/AtomFeat.cpp.o.d -o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/AtomFeat.cpp [ 63%] Linking CXX executable filterCatalogTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so [ 63%] Linking CXX executable chemTransformsTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -o chemTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so [ 63%] Built target filterCatalogTest make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o -MF CMakeFiles/testFingerprints.dir/test1.cpp.o.d -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/test1.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 63%] Built target chemTransformsTestCatch make -f 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directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 63%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -MF CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o.d -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp [ 63%] Linking CXX executable testFragCatalog cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 63%] Built target testFragCatalog make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -MF CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o.d -o 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/catch_tests.cpp [ 63%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp [ 64%] Linking CXX executable testMHFPFingerprint cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 64%] Built target testMHFPFingerprint make -f Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o -MF CMakeFiles/Descriptors.dir/EEM.cpp.o.d -o CMakeFiles/Descriptors.dir/EEM.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/EEM.cpp [ 64%] Linking CXX executable fileParsersCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -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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/usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 65%] Built target fileParsersCatchTest 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o -MF CMakeFiles/testMolTransforms.dir/test1.cpp.o.d -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp [ 65%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp [ 65%] Linking CXX executable fpGenTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -o fpGenTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 65%] Built target fpGenTestCatch 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 65%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp [ 65%] Linking CXX executable fpTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script 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object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -MF CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o.d -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp [ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o -MF CMakeFiles/Descriptors.dir/PBF.cpp.o.d -o CMakeFiles/Descriptors.dir/PBF.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PBF.cpp [ 66%] Linking CXX executable testFingerprintGenerators cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so [ 67%] Linking CXX executable testMMFFForceFieldHelpersMultiThread cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 67%] Built target testFingerprintGenerators [ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o -MF CMakeFiles/Descriptors.dir/PMI.cpp.o.d -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PMI.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 67%] Built target testMMFFForceFieldHelpersMultiThread 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 67%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o cd 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Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -MF CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o.d -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp [ 67%] Linking CXX executable testMolTransforms cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 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/usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so [ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 67%] Built target testMolTransforms 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 67%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd 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Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -MF CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o.d -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp [ 67%] Linking CXX executable depictorCatch cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/depictorCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -o depictorCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a 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/usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 67%] Built target depictorCatch make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/catch_tests.cpp [ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp [ 68%] Linking CXX executable testFingerprints cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -MF CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o.d -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp [ 68%] Linking CXX executable testMMFFForceFieldHelpers cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 68%] Built target testMMFFForceFieldHelpers make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make 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Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD 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../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so [ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/AUTOCORR3D.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 68%] Built target 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp [ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o -MF CMakeFiles/Descriptors.dir/RDF.cpp.o.d -o CMakeFiles/Descriptors.dir/RDF.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/RDF.cpp [ 68%] Linking CXX executable testUFFForceFieldHelpers cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -MF CMakeFiles/testMolCatalog.dir/test1.cpp.o.d -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/test1.cpp [ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o [ 68%] Linking CXX executable molAlignCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -MF CMakeFiles/Descriptors.dir/GETAWAY.cpp.o.d -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp [ 68%] Linking CXX executable distGeomHelpersCatch cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -o distGeomHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -MF CMakeFiles/Descriptors.dir/WHIM.cpp.o.d -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/WHIM.cpp [ 68%] Linking CXX executable testFeatures cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. 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-DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -MF CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/catch_tests.cpp /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp: In function 'Eigen::MatrixXd RDKit::Descriptors::{anonymous}::GetPinv(const Eigen::MatrixXd&)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:280:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'Eigen::Index' {aka 'int'} [-Wsign-compare] 280 | for (unsigned int i = 0; i < A.cols(); ++i) { | ~~^~~~~~~~~~ [ 68%] Linking CXX executable testMolCatalog cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -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-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp [ 71%] Linking CXX executable molInterchangeTest1 cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat 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../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 71%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalButinaCluster.cpp [ 71%] Built target molInterchangeTest1 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 71%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -MF CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o.d -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/MMPA_UnitTest.cpp [ 71%] Linking CXX executable molInterchangeCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -o molInterchangeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 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/usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so [ 71%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 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Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Sort.cpp [ 72%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 72%] Built target Descriptors make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 72%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o -MF CMakeFiles/ChemReactions.dir/Reaction.cpp.o.d -o CMakeFiles/ChemReactions.dir/Reaction.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.cpp [ 72%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp In file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, from /usr/include/boost/python/object/class_metadata.hpp:14, from /usr/include/boost/python/class.hpp:23, from /usr/include/boost/python.hpp:18, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp:11: In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', inlined from 'ValueT boost::python::stl_input_iterator::dereference() const [with ValueT = unsigned int]' at /usr/include/boost/python/stl_iterator.hpp:48:60, inlined from 'static typename Facade::reference boost::iterators::iterator_core_access::dereference(const Facade&) [with Facade = boost::python::stl_input_iterator]' at /usr/include/boost/iterator/iterator_facade.hpp:631:31, inlined from 'boost::iterators::detail::iterator_facade_base::reference boost::iterators::detail::iterator_facade_base::operator*() const [with Derived = boost::python::stl_input_iterator; Value = unsigned int; CategoryOrTraversal = std::input_iterator_tag; Reference = unsigned int; Difference = int]' at /usr/include/boost/iterator/iterator_facade.hpp:737:53, inlined from 'void std::vector<_Tp, _Alloc>::_M_range_initialize(_InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1670:21, inlined from 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:708:23, inlined from 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/RDBoost/Wrap.h:140:15: /usr/include/boost/python/extract.hpp:185:11: warning: '*(unsigned int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ In file included from /usr/include/boost/python.hpp:66: /usr/include/boost/python/stl_iterator.hpp: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = unsigned int]': /usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here 48 | return extract(this->impl_.current().get())(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 73%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp [ 73%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 73%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 73%] Built target rdMMPA make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o -MF CMakeFiles/testDescriptors.dir/test.cpp.o.d -o CMakeFiles/testDescriptors.dir/test.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/test.cpp [ 73%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp [ 73%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp [ 73%] Linking CXX shared library ../../../lib/libRDKitFMCS.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g 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/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 73%] Built target FMCS make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -MF CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o.d -o CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp [ 73%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o cd 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp [ 73%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp [ 74%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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CMakeFiles/testEEM.dir/testEEM.cpp.o.d -o CMakeFiles/testEEM.dir/testEEM.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/testEEM.cpp [ 74%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/RascalMCES.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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,libRDKitRascalMCES.so.1 -o ../../../lib/libRDKitRascalMCES.so.1.2023.09.3 CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build [ 79%] Linking CXX executable testAUTOCORR3D cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR3D.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -MF CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o.d -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/testFMCS_Unit.cpp 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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-std=gnu++17 -MD -MT Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -MF CMakeFiles/FMCStest.dir/testFMCS.cpp.o.d -o CMakeFiles/FMCStest.dir/testFMCS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test/testFMCS.cpp [ 83%] Linking CXX executable chiralityTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp: In function 'boost::python::api::object {anonymous}::degenerateSmartsQueryMolDictHelper(const RDKit::MCSResult&)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:646:19: warning: redundant move in return statement [-Wredundant-move] 646 | return std::move(res); | ~~~~~~~~~^~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:646:19: note: remove 'std::move' call /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp: In function 'RDKit::MolAlign::PyO3A* RDKit::MolAlign::getCrippenO3A(RDKit::ROMol&, RDKit::ROMol&, boost::python::list, boost::python::list, int, int, bool, unsigned int, unsigned int, boost::python::list, boost::python::list)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:453:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] 453 | (python::len(prbCrippenContribs) == prbNAtoms)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:468:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] 468 | (python::len(refCrippenContribs) == refNAtoms)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp: In function 'boost::python::tuple RDKit::MolAlign::getCrippenO3AForConfs(RDKit::ROMol&, RDKit::ROMol&, int, boost::python::list, boost::python::list, int, bool, unsigned int, unsigned int, boost::python::list, boost::python::list)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:529:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] 529 | (python::len(prbCrippenContribs) == prbNAtoms)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:544:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] 544 | (python::len(refCrippenContribs) == refNAtoms)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 83%] Built target chiralityTestsCatch 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 83%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/hashfunctions.cpp /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'std::string testChEMBL_Txt(const char*, double, const char*)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:550:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 550 | fprintf(fres, "%s;%lu;%.1f;%.4f;%u;%u;%s;", test, mols.size(), th, sec, | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet_SMI(const char*, const char*)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1232:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 1232 | fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s;", n, mols.size(), | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1244:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 1244 | fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s\n", n, mols.size(), | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet(const char*, const char*)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1350:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 1350 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1403:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 1403 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1492:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 1492 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u [ 83%] Linking CXX executable descriptorsTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 83%] Built target descriptorsTestCatch make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 83%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -MF CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o.d -o CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/mces_catch.cpp [ 83%] Linking CXX executable testMolAlign cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 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CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so 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/usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 83%] Linking CXX executable testO3AAlign cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 [ 83%] Built target ChemReactions make -f Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build.make Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/depend /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 83%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDeprotect_EXPORTS -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Deprotect.cpp [ 83%] Linking CXX executable FMCStest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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-DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -MF CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o.d -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.cpp [ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -MF CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o.d -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp [ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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target rdRascalMCES 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build 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-DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -MF 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/catch_tests.cpp [ 86%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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testEnumeration ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 86%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -MF CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o.d -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/LinkNode.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 86%] Built target testEnumeration [ 86%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/RepeatUnit.cpp [ 86%] Linking CXX executable graphmolMolOpsTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so [ 86%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Metal.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 86%] Built target graphmolMolOpsTest 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 86%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp [ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp [ 86%] Linking CXX executable molHashCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolHash.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 86%] Built target molHashCatchTest 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 86%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -MF CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o.d -o CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/deprotectTest.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolOps.cpp:36: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 420 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ [ 86%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/MolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Normalize.cpp [ 86%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so cd 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../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 86%] Built target rdMolHash make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 86%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -MF CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o.d -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp [ 86%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -MF CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o.d -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp [ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -MF CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/AtomSymbol.cpp [ 86%] Linking CXX executable deprotectTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/deprotectTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -o deprotectTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDeprotect.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 86%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 86%] Built target deprotectTest [ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp cd 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Validate.cpp [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.cpp [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawText.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawText.cpp [ 89%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDeprotect.so CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o ../../../../lib/libRDKitDeprotect.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 89%] Built target rdDeprotect [ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp In file included from /usr/include/c++/13/algorithm:60, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:506:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:533:42, inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:540:31, inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:633:7, inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/13/bits/stl_uninitialized.h:147:27, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/vector.tcc:814:38, inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1483:19, inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:113:32: /usr/include/c++/13/bits/stl_algobase.h:437:30: warning: 'void* __builtin_memmove(void*, const void*, unsigned int)' writing between 5 and 2147483644 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 437 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/i386-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/list:63, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:16: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = long unsigned int]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = long unsigned int]' at /usr/include/c++/13/bits/alloc_traits.h:482:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:378:33, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:375:7, inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/vector.tcc:805:40, inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1483:19, inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:113:32: /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset [-2147483648, -1] into destination object of size [4, 2147483644] allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextJS.cpp [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextCairo.cpp [ 90%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 90%] Built target rdMolEnumerator [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Charge.cpp [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/MolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Tautomer.cpp [ 90%] Linking CXX executable testMolEnumerator cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a 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../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 90%] Built target testMolEnumerator [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/MolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Fragment.cpp [ 90%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 90%] Built target rdmolops [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFT.cpp [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTCairo.cpp [ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o cd 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp [ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp [ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp [ 91%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp [ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 91%] Built target MarvinParser [ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp [ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && 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../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so [ 94%] Linking CXX executable testMrvToMol cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMrvToMol.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 94%] Built target testMrvToMol 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rdmolfiles.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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-202309.3/obj-i686-linux-gnu' [ 94%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -MF CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o.d -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/TautomerQuery.cpp [ 94%] Linking CXX executable moldraw2DRxnTest1 cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 94%] Built target moldraw2DRxnTest1 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o -MF CMakeFiles/molStandardizeTest.dir/test1.cpp.o.d -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/test1.cpp make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -MF CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o.d -o CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/testNormalize.cpp [ 94%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 94%] Built target TautomerQuery 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o -MF CMakeFiles/molValidateTest.dir/testValidate.cpp.o.d -o CMakeFiles/molValidateTest.dir/testValidate.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/testValidate.cpp [ 95%] Linking CXX executable molStandardizeTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 95%] Built target molStandardizeTest 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o -MF CMakeFiles/molChargeTest.dir/testCharge.cpp.o.d -o CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/testCharge.cpp [ 95%] Linking CXX executable molNormalizeTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl In file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, from /usr/include/boost/python/object/class_metadata.hpp:14, from /usr/include/boost/python/class.hpp:23, from /usr/include/boost/python.hpp:18, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:51:33: /usr/include/boost/python/extract.hpp:185:11: warning: '*(unsigned int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:51:33: note: '' declared here 51 | unsigned int len1 = python::extract(bbs[i].attr("__len__")()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:48:28: /usr/include/boost/python/extract.hpp:185:11: warning: '*(unsigned int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:48:28: note: '' declared here 48 | size_t num_bbs = python::extract(bbs.attr("__len__")()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 95%] Built target molNormalizeTest [ 95%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -MF CMakeFiles/rdchem.dir/Atom.cpp.o.d -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Atom.cpp In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:51:33: /usr/include/boost/python/extract.hpp:185:11: warning: '*(unsigned int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:51:33: note: '' declared here 51 | unsigned int len1 = python::extract(bbs[i].attr("__len__")()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:48:28: /usr/include/boost/python/extract.hpp:185:11: warning: '*(unsigned int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:48:28: note: '' declared here 48 | size_t num_bbs = python::extract(bbs.attr("__len__")()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp: In function 'void RDKit::{anonymous}::pyDictToDoubleMap(boost::python::api::object, std::map&)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:77:57: warning: '*(const double*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 77 | double r = python::extract(tDict.values()[i]); | ^ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:77:57: note: '' declared here 77 | double r = python::extract(tDict.values()[i]); | ^ [ 95%] Linking CXX executable molValidateTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 95%] Built target molValidateTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -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 -Wl,-z,relro -Wl,-z,now CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 95%] Built target molChargeTest 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -MF CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o.d -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/test2.cpp [ 95%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp [ 95%] Linking CXX executable molStandardizeSmallTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 95%] Built target molStandardizeSmallTest 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -MF CMakeFiles/molFragmentTest.dir/testFragment.cpp.o.d -o CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/testFragment.cpp [ 95%] Linking CXX executable molTautomerTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 95%] Built target molTautomerTest [ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MaeMolSupplier.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:22: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 420 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ [ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MaeWriter.cpp [ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -MF CMakeFiles/rdchem.dir/Mol.cpp.o.d -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Mol.cpp [ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o -MF CMakeFiles/rdchem.dir/Conformer.cpp.o.d -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Conformer.cpp [ 96%] Linking CXX executable molFragmentTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 96%] Built target molFragmentTest [ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -MF CMakeFiles/rdchem.dir/RingInfo.cpp.o.d -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/RingInfo.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MaeMolSupplier.cpp:23: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 420 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MaeWriter.cpp:21: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 420 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake "--color=" [ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SDMolSupplier.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/catch_tests.cpp [ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -MF CMakeFiles/rdchem.dir/EditableMol.cpp.o.d -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/EditableMol.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Conformer.cpp:21: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*(const double*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); | ^~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here 68 | T res = python::extract(d_seq[which]); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o cd 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/TDTMolSupplier.cpp [ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp [ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SmilesMolSupplier.cpp [ 96%] Linking CXX executable molStandardizeCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -o molStandardizeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SmilesWriter.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 96%] Built target molStandardizeCatchTest 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake "--color=" make[4]: 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp [ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ 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CMakeFiles/rdchem.dir/MolBundle.cpp.o.d -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolBundle.cpp [ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Validate.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SmilesWriter.cpp:20: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 420 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ [ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o [ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SDWriter.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/TDTWriter.cpp [ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Charge.cpp [ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o [ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/PDBWriter.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o -MF CMakeFiles/rdchem.dir/StereoGroup.cpp.o.d -o CMakeFiles/rdchem.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/StereoGroup.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SDWriter.cpp:21: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 420 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/TDTWriter.cpp:21: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 420 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ [ 98%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp [ 98%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp [ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp [ 98%] Linking CXX executable moldraw2DTest1 cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 98%] Built target moldraw2DTest1 [ 98%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -MF CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SubstanceGroup.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/PDBWriter.cpp:20: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 420 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ In file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, from /usr/include/boost/python/object/class_metadata.hpp:14, from /usr/include/boost/python/class.hpp:23, from /usr/include/boost/python.hpp:18, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/StereoGroup.cpp:12: In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', inlined from 'ValueT boost::python::stl_input_iterator::dereference() const [with ValueT = unsigned int]' at /usr/include/boost/python/stl_iterator.hpp:48:60, inlined from 'static typename Facade::reference boost::iterators::iterator_core_access::dereference(const Facade&) [with Facade = boost::python::stl_input_iterator]' at /usr/include/boost/iterator/iterator_facade.hpp:631:31, inlined from 'boost::iterators::detail::iterator_facade_base::reference boost::iterators::detail::iterator_facade_base::operator*() const [with Derived = boost::python::stl_input_iterator; Value = unsigned int; CategoryOrTraversal = std::input_iterator_tag; Reference = unsigned int; Difference = int]' at /usr/include/boost/iterator/iterator_facade.hpp:737:53, inlined from 'RDKit::StereoGroup* RDKit::{anonymous}::createStereoGroup(RDKit::StereoGroupType, RDKit::ROMol&, boost::python::api::object, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/StereoGroup.cpp:35:22: /usr/include/boost/python/extract.hpp:185:11: warning: '*(unsigned int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ In file included from /usr/include/boost/python.hpp:66: /usr/include/boost/python/stl_iterator.hpp: In function 'RDKit::StereoGroup* RDKit::{anonymous}::createStereoGroup(RDKit::StereoGroupType, RDKit::ROMol&, boost::python::api::object, unsigned int)': /usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here 48 | return extract(this->impl_.current().get())(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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"--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SCAFFOLDNETWORK_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -MF CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o.d -o CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp [ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp [ 98%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so [ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Metal.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 98%] Built target rdmolfiles 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 98%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 98%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -MF CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o.d -o CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp [ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp [ 98%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 98%] Built target ScaffoldNetwork make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 98%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -MF CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/XQMol.cpp 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 98%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp In file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, from /usr/include/boost/python/object/class_metadata.hpp:14, from /usr/include/boost/python/class.hpp:23, from /usr/include/boost/python.hpp:18, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SubstanceGroup.cpp:12: In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, inlined from 'void RDKit::{anonymous}::addBracketHelper(RDKit::SubstanceGroup&, boost::python::api::object)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SubstanceGroup.cpp:65:29: /usr/include/boost/python/extract.hpp:185:11: warning: '*(unsigned int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SubstanceGroup.cpp: In function 'void RDKit::{anonymous}::addBracketHelper(RDKit::SubstanceGroup&, boost::python::api::object)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SubstanceGroup.cpp:65:72: note: '' declared here 65 | unsigned int sz = python::extract(pts.attr("__len__")()); | ^ [ 99%] Linking CXX executable tautomerQueryTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', inlined from 'ValueT boost::python::stl_input_iterator::dereference() const [with ValueT = unsigned int]' at /usr/include/boost/python/stl_iterator.hpp:48:60, inlined from 'static typename Facade::reference boost::iterators::iterator_core_access::dereference(const Facade&) [with Facade = boost::python::stl_input_iterator]' at /usr/include/boost/iterator/iterator_facade.hpp:631:31, inlined from 'boost::iterators::detail::iterator_facade_base::reference boost::iterators::detail::iterator_facade_base::operator*() const [with Derived = boost::python::stl_input_iterator; Value = unsigned int; CategoryOrTraversal = std::input_iterator_tag; Reference = unsigned int; Difference = int]' at /usr/include/boost/iterator/iterator_facade.hpp:737:53, inlined from 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/vector.tcc:303:13, inlined from 'void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:826:17, inlined from 'void pythonObjectToVect(const boost::python::api::object&, std::vector&) [with T = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/RDBoost/Wrap.h:149:15: /usr/include/boost/python/extract.hpp:185:11: warning: '*(unsigned int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ In file included from /usr/include/boost/python.hpp:66: /usr/include/boost/python/stl_iterator.hpp: In function 'void pythonObjectToVect(const boost::python::api::object&, std::vector&) [with T = unsigned int]': /usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here 48 | return extract(this->impl_.current().get())(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', inlined from 'ValueT boost::python::stl_input_iterator::dereference() const [with ValueT = unsigned int]' at /usr/include/boost/python/stl_iterator.hpp:48:60, inlined from 'static typename Facade::reference boost::iterators::iterator_core_access::dereference(const Facade&) [with Facade = boost::python::stl_input_iterator]' at /usr/include/boost/iterator/iterator_facade.hpp:631:31, inlined from 'boost::iterators::detail::iterator_facade_base::reference boost::iterators::detail::iterator_facade_base::operator*() const [with Derived = boost::python::stl_input_iterator; Value = unsigned int; CategoryOrTraversal = std::input_iterator_tag; Reference = unsigned int; Difference = int]' at /usr/include/boost/iterator/iterator_facade.hpp:737:53, inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/vector.tcc:736:22, inlined from 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/vector.tcc:307:19, inlined from 'void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:826:17, inlined from 'void pythonObjectToVect(const boost::python::api::object&, std::vector&) [with T = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/RDBoost/Wrap.h:149:15: /usr/include/boost/python/extract.hpp:185:11: warning: '*(unsigned int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ /usr/include/boost/python/stl_iterator.hpp: In function 'void pythonObjectToVect(const boost::python::api::object&, std::vector&) [with T = unsigned int]': /usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here 48 | return extract(this->impl_.current().get())(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 99%] Built target tautomerQueryTestCatch make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 99%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -MF CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o.d -o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp:15: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 420 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ [ 99%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -MF CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/TextIO.cpp [ 99%] Linking CXX executable testReaction cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl [ 99%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdchem.so CMakeFiles/rdchem.dir/rdchem.cpp.o CMakeFiles/rdchem.dir/Table.cpp.o CMakeFiles/rdchem.dir/Atom.cpp.o CMakeFiles/rdchem.dir/Bond.cpp.o CMakeFiles/rdchem.dir/Mol.cpp.o CMakeFiles/rdchem.dir/Conformer.cpp.o CMakeFiles/rdchem.dir/RingInfo.cpp.o CMakeFiles/rdchem.dir/EditableMol.cpp.o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o CMakeFiles/rdchem.dir/MolBundle.cpp.o CMakeFiles/rdchem.dir/StereoGroup.cpp.o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o CMakeFiles/rdchem.dir/Chirality.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 99%] Built target testReaction [ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o.d -o 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -MF CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o.d -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp [ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupData.cpp [ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 99%] Built target rdTautomerQuery [ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp In file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, from /usr/include/boost/python/object/class_metadata.hpp:14, from /usr/include/boost/python/class.hpp:23, 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-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:11: In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = int]', inlined from 'boost::python::extract::operator result_type() const [with T = int]' at /usr/include/boost/python/extract.hpp:136:23, inlined from 'int {anonymous}::pyobjFunctor::operator()(const RDKit::ROMol&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:218:20, inlined from 'static R boost::detail::function::function_obj_invoker1::invoke(boost::detail::function::function_buffer&, T0) [with FunctionObj = {anonymous}::pyobjFunctor; R = int; T0 = const RDKit::ROMol&]' at /usr/include/boost/function/function_template.hpp:137:22: /usr/include/boost/python/extract.hpp:185:11: warning: '*(int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp: In static member function 'static R boost::detail::function::function_obj_invoker1::invoke(boost::detail::function::function_buffer&, T0) [with FunctionObj = {anonymous}::pyobjFunctor; R = int; T0 = const RDKit::ROMol&]': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:218:54: note: '' declared here 218 | return python::extract(dp_obj(boost::ref(m))); | ^ [ 99%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so cd 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../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 99%] Built target rdMolStandardize [100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && 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Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp [100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp [100%] Linking CXX executable testScaffoldNetwork cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target testScaffoldNetwork [100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupScore.cpp [100%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/GeneralizedSubstruct.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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,libRDKitGeneralizedSubstruct.so.1 -o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitGeneralizedSubstruct.so.1 ../../../lib/libRDKitGeneralizedSubstruct.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target GeneralizedSubstruct [100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp [100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp 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-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -MF CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -MF CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/catch_tests.cpp [100%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target rdScaffoldNetwork make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Building CXX object Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeneralizedSubstruct_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -MF CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o.d -o CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/Wrap/rdGeneralizedSubstruct.cpp [100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -MF CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/PatternFactory.cpp [100%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o 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../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target RGroupDecomposition make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/depend make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/depend make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make 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Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -MF CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o.d -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -MF CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o.d -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp [100%] Linking CXX executable generalizedSubstructCatch cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -o generalizedSubstructCatch 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../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target rdGeneralizedSubstruct [100%] Linking CXX executable testRGroupDecompInternals cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target testRGroupDecompInternals [100%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target SubstructLibrary make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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-202309.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" [100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/catch_tests.cpp [100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp [100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp [100%] Linking CXX executable rgroupCatchTests cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target rgroupCatchTests [100%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../../lib/libRDKitga.so.1.2023.09.3 ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target rdRGroupDecomposition [100%] Linking CXX executable substructLibraryTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target substructLibraryTest [100%] Linking CXX executable substructLibraryCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target substructLibraryCatchTest [100%] Linking CXX executable testRGroupDecomp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target testRGroupDecomp In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:36: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here 185 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 420 | result = off_type(bp::extract(py_tell())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ [100%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target rdMolDraw2D [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target rdSubstructLibrary [100%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target rdChemReactions [100%] Linking CXX executable moldraw2DTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target moldraw2DTestCatch make[3]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' STATIC_LINK=0 RDKIT_LIBDIR=/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu//lib pg_buildext build /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit build-%v ### PostgreSQL 16 build ### make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/build-16' gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/rdkit_io.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/mol_op.c /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'mol_murckoscaffold': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:406:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 406 | CROMol scaffold = MolMurckoScaffold(mol); | ^~~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'mol_nm_hash': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:426:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 426 | char *str = computeNMMolHash(mol, opts); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:428:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 428 | char *res = pnstrdup(str, strlen(str)); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:421:7: warning: unused variable 'len' [-Wunused-variable] 421 | int len; | ^~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'mol_adjust_query_properties': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:441:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 441 | char *data = PG_GETARG_CSTRING(1); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:447:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 447 | Mol *res = deconstructROMolWithQueryProperties(adj); | ^~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'mol_to_svg': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:462:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 462 | char *legend = PG_GETARG_CSTRING(1); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'mol_to_xqmol': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:482:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 482 | bool doEnumeration = PG_GETARG_BOOL(1); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:493:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 493 | XQMol *res = deconstructXQMol(xqm); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_smiles': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:512:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 512 | char *res = pnstrdup(str, strlen(str)); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mol2s_transition': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:580:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 580 | text *ts = (text *)palloc(ts_size); // new return value | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:600:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 600 | char *smiles = makeMolText(mol, &len, false, false); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mols': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:638:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 638 | int32 ts_size = VARHDRSZ + strlen(str); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_smiles_transition': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:544:1: warning: control reaches end of non-void function [-Wreturn-type] 544 | } | ^ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mol_transition': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:679:1: warning: control reaches end of non-void function [-Wreturn-type] 679 | } | ^ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/bfp_op.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/sfp_op.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/rxn_op.c /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rxn_op.c:134:3: warning: multi-line comment [-Wcomment] 134 | // /* keep compiler quiet - no extra ; */ \ | ^ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rxn_op.c: In function 'reaction_to_svg': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rxn_op.c:149:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 149 | bool highlightByReactants = PG_GETARG_BOOL(1); | ^~~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/rdkit_gist.c /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'soergeldistsign': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:219:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 219 | uint8 *as = (uint8 *)VARDATA(a); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'soergeldist': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:238:10: warning: unused variable 'd' [-Wunused-variable] 238 | double d; | ^ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'gmol_consistent': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:484:9: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 484 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:496:9: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 496 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:526:9: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 526 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'gmol_cmp': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:555:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 555 | int siglen = SIGLEN(a); | ^~~ In file included from /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit.h:44, from /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:40: /usr/include/postgresql/16/server/varatt.h:244:68: warning: pointer targets in passing argument 2 of 'bitstringGrayCmp' differ in signedness [-Wpointer-sign] 244 | #define VARDATA_4B(PTR) (((varattrib_4b *) (PTR))->va_4byte.va_data) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ | | | char * /usr/include/postgresql/16/server/varatt.h:278:65: note: in expansion of macro 'VARDATA_4B' 278 | #define VARDATA(PTR) VARDATA_4B(PTR) | ^~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:558:41: note: in expansion of macro 'VARDATA' 558 | int retval = bitstringGrayCmp(siglen, VARDATA(a), VARDATA(b)); | ^~~~~~~ In file included from /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:43: /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.h:60:41: note: expected 'uint8 *' {aka 'unsigned char *'} but argument is of type 'char *' 60 | int bitstringGrayCmp(int length, uint8 *bstr1, uint8 *bstr2); | ~~~~~~~^~~~~ /usr/include/postgresql/16/server/varatt.h:244:68: warning: pointer targets in passing argument 3 of 'bitstringGrayCmp' differ in signedness [-Wpointer-sign] 244 | #define VARDATA_4B(PTR) (((varattrib_4b *) (PTR))->va_4byte.va_data) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ | | | char * /usr/include/postgresql/16/server/varatt.h:278:65: note: in expansion of macro 'VARDATA_4B' 278 | #define VARDATA(PTR) VARDATA_4B(PTR) | ^~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:558:53: note: in expansion of macro 'VARDATA' 558 | int retval = bitstringGrayCmp(siglen, VARDATA(a), VARDATA(b)); | ^~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.h:60:55: note: expected 'uint8 *' {aka 'unsigned char *'} but argument is of type 'char *' 60 | int bitstringGrayCmp(int length, uint8 *bstr1, uint8 *bstr2); | ~~~~~~~^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:558:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 558 | int retval = bitstringGrayCmp(siglen, VARDATA(a), VARDATA(b)); | ^~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'rdkit_consistent': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:643:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 643 | int siglen = SIGLEN(query); | ^~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:657:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 657 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'gsfp_consistent': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:689:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 689 | int sum, overlapSum, overlapN; | ^~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:693:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 693 | int nKey = (ISALLTRUE(key)) | ^~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'greaction_consistent': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:757:9: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 757 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:774:9: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 774 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:800:9: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 800 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c: At top level: /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:631:13: warning: 'rdkit_consistent' defined but not used [-Wunused-function] 631 | static bool rdkit_consistent(GISTENTRY *entry, StrategyNumber strategy, | ^~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:237:12: warning: 'soergeldist' defined but not used [-Wunused-function] 237 | static int soergeldist(bytea *a, bytea *b) { | ^~~~~~~~~~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/bfp_gist.c /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_gist.c: In function 'gbfp_cmp': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_gist.c:659:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 659 | GBfp *gbfp2 = (GBfp *)PG_DETOAST_DATUM(y); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_gist.c:662:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 662 | int siglen = GBFP_LEAF_SIGLEN(gbfp1); | ^~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_gist.c:665:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 665 | int retval = bitstringGrayCmp(siglen, GET_LEAF_DATA(gbfp1)->fp, GET_LEAF_DATA(gbfp2)->fp); | ^~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_gist.c: In function 'merge_key': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_gist.c:689:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 689 | int siglen = GBFP_INNER_SIGLEN(result); | ^~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/bfp_gin.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/low_gist.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/guc.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/cache.c g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/adapter.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/bitstring.c /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.c: In function 'bitstringUnion': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.c:64:7: warning: unused variable 'i' [-Wunused-variable] 64 | int i; | ^ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.c: In function 'bitstringIntersection': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.c:96:7: warning: unused variable 'i' [-Wunused-variable] 96 | int i; | ^ g++ -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -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-16/lib -Wl,--as-needed -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -L/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu//lib -lRDKitGeneralizedSubstruct -lRDKitMolEnumerator -lRDKitTautomerQuery -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_MOL_GIST_SORTSUPPORT@/FUNCTION 11 gmol_sortsupport (internal),/' \ -e's/@RDKIT_PG_QMOL_GIST_SORTSUPPORT@/FUNCTION 11 gmol_sortsupport (internal),/' \ -e's/@RDKIT_PG_BFP_GIST_SORTSUPPORT@/FUNCTION 11 gbfp_sortsupport (internal),/' \ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit.sql.in > rdkit--4.4.0.sql /usr/bin/clang-16 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Xclang -no-opaque-pointers -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/rdkit_io.c /usr/bin/clang-16 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Xclang -no-opaque-pointers -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/mol_op.c /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:544:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:679:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 2 warnings generated. /usr/bin/clang-16 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Xclang -no-opaque-pointers -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/bfp_op.c /usr/bin/clang-16 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Xclang -no-opaque-pointers -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/sfp_op.c /usr/bin/clang-16 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Xclang -no-opaque-pointers -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/rxn_op.c /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rxn_op.c:100:37: warning: passing arguments to 'ReactionSubstructFP' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] PG_RETURN_BOOL(ReactionSubstructFP(rxn, rxn2)); ^ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rxn_op.c:115:37: warning: passing arguments to 'ReactionSubstructFP' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] PG_RETURN_BOOL(ReactionSubstructFP(rxn2, rxn)); ^ 2 warnings generated. /usr/bin/clang-16 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Xclang -no-opaque-pointers -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/rdkit_gist.c /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:558:41: warning: passing 'char[]' to parameter of type 'uint8 *' (aka 'unsigned char *') converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign] int retval = bitstringGrayCmp(siglen, VARDATA(a), VARDATA(b)); ^~~~~~~~~~ /usr/include/postgresql/16/server/varatt.h:278:27: note: expanded from macro 'VARDATA' #define VARDATA(PTR) VARDATA_4B(PTR) ^~~~~~~~~~~~~~~ /usr/include/postgresql/16/server/varatt.h:244:26: note: expanded from macro 'VARDATA_4B' #define VARDATA_4B(PTR) (((varattrib_4b *) (PTR))->va_4byte.va_data) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.h:60:41: note: passing argument to parameter 'bstr1' here int bitstringGrayCmp(int length, uint8 *bstr1, uint8 *bstr2); ^ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:558:53: warning: passing 'char[]' to parameter of type 'uint8 *' (aka 'unsigned char *') converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign] int retval = bitstringGrayCmp(siglen, VARDATA(a), VARDATA(b)); ^~~~~~~~~~ /usr/include/postgresql/16/server/varatt.h:278:27: note: expanded from macro 'VARDATA' #define VARDATA(PTR) VARDATA_4B(PTR) ^~~~~~~~~~~~~~~ /usr/include/postgresql/16/server/varatt.h:244:26: note: expanded from macro 'VARDATA_4B' #define VARDATA_4B(PTR) (((varattrib_4b *) (PTR))->va_4byte.va_data) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.h:60:55: note: passing argument to parameter 'bstr2' here int bitstringGrayCmp(int length, uint8 *bstr1, uint8 *bstr2); ^ 2 warnings generated. /usr/bin/clang-16 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Xclang -no-opaque-pointers -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/bfp_gist.c /usr/bin/clang-16 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Xclang -no-opaque-pointers -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/bfp_gin.c /usr/bin/clang-16 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Xclang -no-opaque-pointers -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/low_gist.c /usr/bin/clang-16 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Xclang -no-opaque-pointers -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/guc.c /usr/bin/clang-16 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Xclang -no-opaque-pointers -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/cache.c /usr/bin/clang-16 -std=c++17 -xc++ -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Xclang -no-opaque-pointers -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/adapter.cpp /usr/lib/llvm-16/bin/opt -module-summary -f adapter.bc -o adapter.bc /usr/bin/clang-16 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Xclang -no-opaque-pointers -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/16/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-202309.3/Code/PgSQL/rdkit/bitstring.c make[2]: Leaving directory '/build/reproducible-path/rdkit-202309.3/build-16' ### End 16 build ### (cd /build/reproducible-path/rdkit-202309.3/Code; doxygen doxygen/doxygen.config) warning: Tag 'TCL_SUBST' at line 213 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'SYMBOL_CACHE_SIZE' at line 337 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'SHOW_DIRECTORIES' at line 557 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'COLS_IN_ALPHA_INDEX' at line 869 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'HTML_TIMESTAMP' at line 965 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 'FORMULA_TRANSPARENT' at line 1189 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'LATEX_SOURCE_CODE' at line 1327 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_SCHEMA' at line 1425 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_DTD' at line 1431 of file 'doxygen/doxygen.config' has become obsolete. 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 'CLASS_DIAGRAMS' at line 1608 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: Tag 'DOT_FONTNAME' at line 1647 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 'DOT_FONTSIZE' at line 1652 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 'DOT_TRANSPARENT' at line 1792 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: 1.9.8 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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in directory /build/reproducible-path/rdkit-202309.3/Code/ML/Data Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/DataManip Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/RDGeneral Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/hash Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/hash/detail Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/RDBoost Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/DistGeom Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ForceField Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics/EigenSolvers Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Geometry Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Features Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures Reading and parsing tag files Parsing files Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Abbreviations.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Abbreviations.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/atomic_data.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/atomic_data.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/AtomIterators.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/AtomIterators.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Bond.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Bond.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/BondIterators.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/BondIterators.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Canon.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Canon.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/CartesianProduct.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/CartesianProduct.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/Enumerate.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/Enumerate.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/RandomSample.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/RandomSample.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/PreprocessRxn.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/PreprocessRxn.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionFingerprints.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionFingerprints.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionParser.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionParser.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionPickler.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionPickler.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionRunner.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionRunner.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/SanitizeRxn.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/SanitizeRxn.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/ChemTransforms.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/ChemTransforms.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/MolFragmenter.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/MolFragmenter.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPLabeler.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPLabeler.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPMol.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPMol.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Configuration.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Configuration.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Descriptor.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Descriptor.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Digraph.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Digraph.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Edge.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Edge.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Mancude.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Mancude.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Node.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Node.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Priority.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Priority.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Pairlist.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Pairlist.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1a.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1a.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1b.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1b.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule2.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule2.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule3.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule3.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4a.h... 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Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/CoulombMat.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/CoulombMat.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Crippen.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Crippen.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/EEM.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/EEM.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Lipinski.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Lipinski.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolDescriptors.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolDescriptors.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolDescriptors3D.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolDescriptors3D.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolSurf.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolSurf.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MORSE.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MORSE.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MQN.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MQN.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/OxidationNumbers.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/OxidationNumbers.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PBF.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PBF.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PMI.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PMI.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Property.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Property.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/RDF.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/RDF.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/RegisterDescriptor.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/RegisterDescriptor.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/USRDescriptor.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/USRDescriptor.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/WHIM.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/WHIM.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/details.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/details.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DetermineBonds/DetermineBonds.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DetermineBonds/DetermineBonds.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Embedder.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Embedder.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/CDXMLParser.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/CDXMLParser.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/FileParsers.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/FileParsers.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/FileParserUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/FileParserUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/GeneralFileReader.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/GeneralFileReader.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileStereochem.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileStereochem.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupParsing.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupParsing.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupWriting.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupWriting.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSupplier.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolWriters.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolWriters.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/PNGParser.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/PNGParser.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/ProximityBonds.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/ProximityBonds.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceParsers.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceParsers.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceWriters.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceWriters.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalog.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalog.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatchers.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatchers.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Filters.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Filters.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Fingerprints.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Fingerprints.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintUtil.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintUtil.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MACCS.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MACCS.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MHFP.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MHFP.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganFingerprints.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganFingerprints.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Composition2N.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Composition2N.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/DebugTrace.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/DebugTrace.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/FMCS.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/FMCS.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Graph.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Graph.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/MatchTable.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/MatchTable.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Seed.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Seed.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SeedSet.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SeedSet.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SubstructMatchCustom.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SubstructMatchCustom.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SubstructureCache.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SubstructureCache.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Target.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Target.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/TargetMatch.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/TargetMatch.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/FFConvenience.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/FFConvenience.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatGenerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatGenerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragFPGenerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragFPGenerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/XQMol.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/XQMol.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups/GenericGroups.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups/GenericGroups.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GraphMol.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GraphMol.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinDefs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinDefs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinParser.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinParser.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/MMPA.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/MMPA.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/AlignMolecules.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/AlignMolecules.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolBundle.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolBundle.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalog.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalog.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Graph/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:233: warning: unbalanced grouping commands Mol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/AtomSymbol.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/AtomSymbol.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawAnnotation.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawAnnotation.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCH.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCH.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawText.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawText.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextCairo.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextCairo.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFT.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFT.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTCairo.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTCairo.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTJS.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTJS.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextJS.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextJS.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextNotFT.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextNotFT.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextSVG.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextSVG.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Fonts/roboto_regular.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Fonts/roboto_regular.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Fonts/telex_regular.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Fonts/telex_regular.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDr/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.h:440: warning: unbalanced grouping commands /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.h:692: warning: unbalanced grouping commands aw2D/MolDraw2DDetails.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DJS.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DJS.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Qt/DrawTextFTQt.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Qt/DrawTextFTQt.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Qt/DrawTextQt.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Qt/DrawTextQt.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Qt/MolDraw2DQt.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Qt/MolDraw2DQt.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/StringRect.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/StringRect.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/LinkNode.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/LinkNode.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/mf.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/mf.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/MolHash.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/MolHash.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/nmmolhash.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/nmmolhash.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/details.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/details.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/MolInterchange.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/MolInterchange.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Charge.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Charge.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Fragment.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Fragment.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Metal.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Metal.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/MolStandardize.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/MolStandardize.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Normalize.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Normalize.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Tautomer.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Tautomer.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Validate.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Validate.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/MolTransforms.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/MolTransforms.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MonomerInfo.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MonomerInfo.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/new_canon.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/new_canon.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/GasteigerCharges.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/GasteigerCharges.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/GasteigerParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/GasteigerParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryAtom.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryAtom.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryBond.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryBond.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/PartitionSet.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/PartitionSet.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalClusterOptions.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalClusterOptions.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalDetails.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalDetails.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalMCES.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalMCES.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalOptions.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalOptions.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalResult.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalResult.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitQueries.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitQueries.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Resonance.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Resonance.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupCore.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupCore.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupData.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupData.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition//build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h:416: warning: unbalanced grouping commands RGroupDecompParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupGa.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupGa.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupMatch.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupMatch.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupScore.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupScore.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RingInfo.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RingInfo.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Rings.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Rings.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SanitException.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SanitException.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/detail.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/detail.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNAttribs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNAttribs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNParse.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNParse.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNParseOps.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNParseOps.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/primes.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/primes.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmartsWrite.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmartsWrite.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParse.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParse.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParseOps.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParseOps.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StereoGroup.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StereoGroup.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/Pattern.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/Pattern.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/ReCharge.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/ReCharge.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/Stereo.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/Stereo.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/StripSmallFragments.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/StripSmallFragments.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/StructChecker.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/StructChecker.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/StructCheckerOptions.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/StructCheckerOptions.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/Tautomer.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/Tautomer.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/Utilites.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/Utilites.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/Subgraphs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/Subgraphs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/SubgraphUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/SubgraphUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstanceGroup.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstanceGroup.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructMatch.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructMatch.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/PatternFactory.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/PatternFactory.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/TautomerQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/TautomerQuery.h... 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Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/base64.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitOps.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitOps.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitVect.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitVect.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitVects.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitVects.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitVectUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitVectUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DatastructsException.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DatastructsException.h... 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Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/GreaterEqualQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/GreaterQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/GreaterQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/LessEqualQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/LessEqualQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/LessQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/LessQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/NullQueryAlgebra.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/NullQueryAlgebra.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/OrQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/OrQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/Query.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/Query.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/QueryObjects.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/QueryObjects.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/RangeQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/RangeQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/SetQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/SetQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/XOrQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/XOrQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/CorrMatGenerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/CorrMatGenerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/InfoBitRanker.h... 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Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Params.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/StretchBend.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/StretchBend.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionAngle.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionAngle.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleBend.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleBend.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleConstraint.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleConstraint.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/BondStretch.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/BondStretch.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Contribs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Contribs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/DistanceConstraint.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/DistanceConstraint.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Inversion.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Inversion.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Nonbonded.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Nonbonded.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Params.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Params.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/TorsionAngle.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/TorsionAngle.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/AlignPoints.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/AlignPoints.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Numerics/Conrec.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Numerics/Conrec.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Numerics/Matrix.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Numerics/Matrix.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Numerics/SquareMatrix.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Numerics/SquareMatrix.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Numerics/SymmMatrix.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Numerics/SymmMatrix.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Numerics/Vector.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Numerics/Vector.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Geometry/Grid3D.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Geometry/Grid3D.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Geometry/GridUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Geometry/GridUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Geometry/point.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Geometry/point.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform2D.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform2D.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform3D.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform3D.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Geometry/UniformGrid3D.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Geometry/UniformGrid3D.h... Pr/build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h:62: warning: documented symbol 'for experimental torsion angle RDKit::DGeomHelpers::preferences' was not declared or defined. /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.h:1082: warning: documented symbol 'modifies molecule in RDKit::MolOps::place' was not declared or defined. /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.h:1098: warning: documented symbol 'modifies molecule in RDKit::MolOps::place' was not declared or defined. /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h:93: warning: no matching file member found for RDKIT_RGROUPDECOMPOSITION_EXPORT std::string RDKit::toJSON(const std::map &rgr, const std::string &prefix="") Possible candidates: 'RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupRow &rgr, const std::string &prefix="")' at line 81 of file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h 'RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupRows &rgr, const std::string &prefix="")' at line 85 of file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h 'RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupColumn &rgr, const std::string &prefix="")' at line 89 of file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:525: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:534: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override' eprocessing /build/reproducible-path/rdkit-202309.3/Code/Geometry/Utils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Geometry/Utils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Features/Feature.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Features/Feature.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/ChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/ChemicalFeature.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/FreeChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/FreeChemicalFeature.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Associating documentation with modules... 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... Computing module relations... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file Catalog.h... Generating code for file CatalogEntry.h... Generating code for file CatalogParams.h... Generating code for file ChemicalFeature.h... Generating code for file FreeChemicalFeature.h... Generating code for file MetricFuncs.h... Generating code for file MetricMatrixCalc.h... Generating code for file base64.h... Generating code for file BitOps.h... Generating code for file BitVect.h... Generating code for file BitVects.h... Generating code for file BitVectUtils.h... Generating code for file DatastructsException.h... Generating code for file DatastructsStreamOps.h... Generating code for file DiscreteDistMat.h... Generating code for file DiscreteValueVect.h... Generating code for file ExplicitBitVect.h... Generating code for file FPBReader.h... Generating code for file MultiFPBReader.h... Generating code for file SparseBitVect.h... Generating code for file SparseIntVect.h... Generating code for file BoundsMatrix.h... Generating code for file ChiralSet.h... Generating code for file ChiralViolationContrib.h... Generating code for file DistGeomUtils.h... Generating code for file DistViolationContrib.h... Generating code for file FourthDimContrib.h... Generating code for file TriangleSmooth.h... Generating code for file Feature.h... Generating code for file Contrib.h... Generating code for file ForceField.h... Generating code for file AngleBend.h... Generating code for file AngleBend.h... Generating code for file AngleConstraint.h... Generating code for file AngleConstraint.h... Generating code for file BondStretch.h... Generating code for file BondStretch.h... Generating code for file Contribs.h... Generating code for file Contribs.h... Generating code for file DistanceConstraint.h... Generating code for file DistanceConstraint.h... Generating code for file Nonbonded.h... Generating code for file Nonbonded.h... Generating code for file OopBend.h... Generating code for file Params.h... Generating code for file Params.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... Generating code for file StretchBend.h... Generating code for file TorsionAngle.h... Generating code for file TorsionAngle.h... Generating code for file TorsionConstraint.h... Generating code for file TorsionConstraint.h... Generating code for file Inversion.h... Generating code for file Grid3D.h... Generating code for file GridUtils.h... Generating code for file point.h... Generating code for file Transform.h... Generating code for file Transform2D.h... Generating code for file Transform3D.h... Generating code for file UniformGrid3D.h... Generating code for file Utils.h... Generating code for file Abbreviations.h... Generating code for file Atom.h... Generating code for file atomic_data.h... Generating code for file AtomIterators.h... Generating code for file Bond.h... Generating code for file BondIterators.h... Generating code for file Canon.h... Generating code for file CartesianProduct.h... Generating code for file Enumerate.h... Generating code for file EnumerateBase.h... Generating code for file EnumerateTypes.h... Generating code for file EnumerationPickler.h... Generating code for file EnumerationStrategyBase.h... Generating code for file EvenSamplePairs.h... Generating code for file RandomSample.h... Generating code for file RandomSampleAllBBs.h... Generating code for file PreprocessRxn.h... Generating code for file Reaction.h... Generating code for file ReactionFingerprints.h... Generating code for file ReactionParser.h... Generating code for file ReactionPickler.h... Generating code for file ReactionRunner.h... Generating code for file ReactionUtils.h... Generating code for file SanitizeRxn.h... Generating code for file ChemTransforms.h... Generating code for file MolFragmenter.h... Generating code for file Chirality.h... Generating code for file CIPLabeler.h... Generating code for file CIPMol.h... Generating code for file Configuration.h... Generating code for file Sp2Bond.h... Generating code for file Tetrahedral.h... Generating code for file Descriptor.h... Generating code for file Digraph.h... Generating code for file Edge.h... Generating code for file Mancude.h... Generating code for file Node.h... Generating code for file Priority.h... Generating code for file Pairlist.h... Generating code for file Rule1a.h... Generating code for file Rule1b.h... Generating code for file Rule2.h... Generating code for file Rule3.h... Generating code for file Rule4a.h... Generating code for file Rule4b.h... Generating code for file Rule4c.h... Generating code for file Rule5.h... Generating code for file Rule5New.h... Generating code for file Rule6.h... Generating code for file Rules.h... Generating code for file SequenceRule.h... Generating code for file Sort.h... Generating code for file TooManyNodesException.h... Generating code for file Conformer.h... Generating code for file DepictUtils.h... Generating code for file EmbeddedFrag.h... Generating code for file RDDepictor.h... Generating code for file Templates.h... Generating code for file TemplateSmiles.h... Generating code for file Deprotect.h... Generating code for file AtomFeat.h... Generating code for file AUTOCORR2D.h... Generating code for file AUTOCORR3D.h... Generating code for file BCUT.h... Generating code for file ConnectivityDescriptors.h... Generating code for file CoulombMat.h... Generating code for file Crippen.h... Generating code for file Data3Ddescriptors.h... Generating code for file EEM.h... Generating code for file GETAWAY.h... Generating code for file Lipinski.h... Generating code for file MolData3Ddescriptors.h... Generating code for file MolDescriptors.h... Generating code for file MolDescriptors3D.h... Generating code for file MolSurf.h... Generating code for file MORSE.h... Generating code for file MQN.h... Generating code for file OxidationNumbers.h... Generating code for file PBF.h... Generating code for file PMI.h... Generating code for file Property.h... Generating code for file RDF.h... Generating code for file RegisterDescriptor.h... Generating code for file USRDescriptor.h... Generating code for file WHIM.h... Generating code for file details.h... Generating code for file details.h... Generating code for file DetermineBonds.h... Generating code for file BoundsMatrixBuilder.h... Generating code for file Embedder.h... Generating code for file CDXMLParser.h... Generating code for file FileParsers.h... Generating code for file FileParserUtils.h... Generating code for file GeneralFileReader.h... Generating code for file MolFileStereochem.h... Generating code for file MolSGroupParsing.h... Generating code for file MolSGroupWriting.h... Generating code for file MolSupplier.h... Generating code for file MolWriters.h... Generating code for file MultithreadedMolSupplier.h... Generating code for file MultithreadedSDMolSupplier.h... Generating code for file MultithreadedSmilesMolSupplier.h... Generating code for file PNGParser.h... Generating code for file ProximityBonds.h... Generating code for file SequenceParsers.h... Generating code for file SequenceWriters.h... Generating code for file FilterCatalog.h... Generating code for file FilterCatalogEntry.h... Generating code for file FilterMatcherBase.h... Generating code for file FilterMatchers.h... Generating code for file Filters.h... Generating code for file FunctionalGroupHierarchy.h... Generating code for file AtomPairGenerator.h... Generating code for file AtomPairs.h... Generating code for file FingerprintGenerator.h... Generating code for file Fingerprints.h... Generating code for file FingerprintUtil.h... Generating code for file MACCS.h... Generating code for file MHFP.h... Generating code for file MorganFingerprints.h... Generating code for file MorganGenerator.h... Generating code for file RDKitFPGenerator.h... Generating code for file TopologicalTorsionGenerator.h... Generating code for file Composition2N.h... Generating code for file DebugTrace.h... Generating code for file DuplicatedSeedCache.h... Generating code for file FMCS.h... Generating code for file Graph.h... Generating code for file MatchTable.h... Generating code for file MaximumCommonSubgraph.h... Generating code for file Seed.h... Generating code for file SeedSet.h... Generating code for file SubstructMatchCustom.h... Generating code for file SubstructureCache.h... Generating code for file Target.h... Generating code for file TargetMatch.h... Generating code for file TorsionAngleM6.h... Generating code for file TorsionPreferences.h... Generating code for file FFConvenience.h... Generating code for file AtomTyper.h... Generating code for file AtomTyper.h... Generating code for file Builder.h... Generating code for file Builder.h... Generating code for file MMFF.h... Generating code for file UFF.h... Generating code for file FragCatalogEntry.h... Generating code for file FragCatalogUtils.h... Generating code for file FragCatGenerator.h... Generating code for file FragCatParams.h... Generating code for file FragFPGenerator.h... Generating code for file XQMol.h... Generating code for file GenericGroups.h... Generating code for file GraphMol.h... Generating code for file MarvinDefs.h... Generating code for file MarvinParser.h... Generating code for file MMPA.h... Generating code for file AlignMolecules.h... Generating code for file O3AAlignMolecules.h... Generating code for file MolBundle.h... Generating code for file MolCatalog.h... Generating code for file MolCatalogEntry.h... Generating code for file MolCatalogParams.h... Generating code for file FeatureParser.h... Generating code for file MolChemicalFeature.h... Generating code for file MolChemicalFeatureDef.h... Generating code for file MolChemicalFeatureFactory.h... Generating code for file AtomSymbol.h... Generating code for file DrawAnnotation.h... Generating code for file DrawMol.h... Generating code for file DrawMolMCH.h... Generating code for file DrawMolMCHCircleAndLine.h... Generating code for file DrawMolMCHLasso.h... Generating code for file DrawShape.h... Generating code for file DrawText.h... Generating code for file DrawTextCairo.h... Generating code for file DrawTextFT.h... Generating code for file DrawTextFTCairo.h... Generating code for file DrawTextFTJS.h... Generating code for file DrawTextFTSVG.h... Generating code for file DrawTextJS.h... Generating code for file DrawTextNotFT.h... Generating code for file DrawTextSVG.h... Generating code for file roboto_regular.h... Generating code for file telex_regular.h... Generating code for file MolDraw2D.h... Generating code for file MolDraw2DCairo.h... Generating code for file MolDraw2DDetails.h... Generating code for file MolDraw2DHelpers.h... Generating code for file MolDraw2DJS.h... Generating code for file MolDraw2DSVG.h... Generating code for file MolDraw2DUtils.h... Generating code for file MolDraw2Dwx.h... Generating code for file DrawTextFTQt.h... Generating code for file DrawTextQt.h... Generating code for file MolDraw2DQt.h... Generating code for file StringRect.h... Generating code for file LinkNode.h... Generating code for file MolEnumerator.h... Generating code for file mf.h... Generating code for file MolHash.h... Generating code for file nmmolhash.h... Generating code for file MolInterchange.h... Generating code for file MolOps.h... Generating code for file MolPickler.h... Generating code for file AcidBaseCatalogEntry.h... Generating code for file AcidBaseCatalogParams.h... Generating code for file AcidBaseCatalogUtils.h... Generating code for file Charge.h... Generating code for file Fragment.h... Generating code for file FragmentCatalogEntry.h... Generating code for file FragmentCatalogParams.h... Generating code for file FragmentCatalogUtils.h... Generating code for file Metal.h... Generating code for file MolStandardize.h... Generating code for file Normalize.h... Generating code for file Tautomer.h... Generating code for file Tautomer.h... Generating code for file TautomerCatalogEntry.h... Generating code for file TautomerCatalogParams.h... Generating code for file TautomerCatalogUtils.h... Generating code for file TransformCatalogEntry.h... Generating code for file TransformCatalogParams.h... Generating code for file TransformCatalogUtils.h... Generating code for file Validate.h... Generating code for file MolTransforms.h... Generating code for file MonomerInfo.h... Generating code for file new_canon.h... Generating code for file GasteigerCharges.h... Generating code for file GasteigerParams.h... Generating code for file PeriodicTable.h... Generating code for file QueryAtom.h... Generating code for file QueryBond.h... Generating code for file QueryOps.h... Generating code for file PartitionSet.h... Generating code for file RascalClusterOptions.h... Generating code for file RascalDetails.h... Generating code for file RascalMCES.h... Generating code for file RascalOptions.h... Generating code for file RascalResult.h... Generating code for file RDKitBase.h... Generating code for file RDKitQueries.h... Generating code for file ReducedGraphs.h... Generating code for file Resonance.h... Generating code for file RGroupCore.h... Generating code for file RGroupData.h... Generating code for file RGroupDecomp.h... Generating code for file RGroupDecompData.h... Generating code for file RGroupDecompParams.h... Generating code for file RGroupFingerprintScore.h... Generating code for file RGroupGa.h... Generating code for file RGroupMatch.h... Generating code for file RGroupScore.h... Generating code for file RGroupUtils.h... Generating code for file RingInfo.h... Generating code for file Rings.h... Generating code for file ROMol.h... Generating code for file RWMol.h... Generating code for file SanitException.h... Generating code for file detail.h... Generating code for file ScaffoldNetwork.h... Generating code for file ShapeEncoder.h... Generating code for file ShapeUtils.h... Generating code for file SLNAttribs.h... Generating code for file SLNParse.h... Generating code for file SLNParseOps.h... Generating code for file primes.h... Generating code for file SmartsWrite.h... Generating code for file SmilesParse.h... Generating code for file SmilesParseOps.h... Generating code for file SmilesWrite.h... Generating code for file StereoGroup.h... Generating code for file Pattern.h... Generating code for file ReCharge.h... Generating code for file Stereo.h... Generating code for file StripSmallFragments.h... Generating code for file StructChecker.h... Generating code for file StructCheckerOptions.h... Generating code for file Utilites.h... Generating code for file Subgraphs.h... Generating code for file SubgraphUtils.h... Generating code for file SubstanceGroup.h... Generating code for file SubstructMatch.h... Generating code for file SubstructUtils.h... Generating code for file PatternFactory.h... Generating code for file SubstructLibrary.h... Generating code for file SubstructLibrarySerialization.h... Generating code for file TautomerQuery.h... Generating code for file Snapshot.h... Generating code for file Trajectory.h... Generating code for file CorrMatGenerator.h... Generating code for file InfoBitRanker.h... Generating code for file InfoGainFuncs.h... Generating code for file AlignPoints.h... Generating code for file Conrec.h... Generating code for file PowerEigenSolver.h... Generating code for file Matrix.h... Generating code for file BFGSOpt.h... Generating code for file SquareMatrix.h... Generating code for file SymmMatrix.h... Generating code for file Vector.h... Generating code for file AndQuery.h... Generating code for file EqualityQuery.h... Generating code for file GreaterEqualQuery.h... Generating code for file GreaterQuery.h... Generating code for file LessEqualQuery.h... Generating code for file LessQuery.h... Generating code for file NullQueryAlgebra.h... Generating code for file OrQuery.h... Generating code for file Query.h... Generating code for file QueryObjects.h... Generating code for file RangeQuery.h... Generating code for file SetQuery.h... Generating code for file XOrQuery.h... Generating code for file boost_numpy.h... Generating code for file import_array.h... Generating code for file pyint_api.h... Generating code for file PySequenceHolder.h... Generating code for file python.h... Generating code for file python_streambuf.h... Generating code for file BadFileException.h... Generating code for file BoostEndInclude.h... Generating code for file BoostStartInclude.h... Generating code for file ConcurrentQueue.h... Generating code for file Dict.h... Generating code for file Exceptions.h... Generating code for file export.h... Generating code for file FileParseException.h... Generating code for file hanoiSort.h... Generating code for file Invariant.h... Generating code for file LocaleSwitcher.h... Generating code for file Ranking.h... Generating code for file RDAny.h... Generating code for file RDConfig.h... Generating code for file RDExportMacros.h... Generating code for file RDLog.h... Generating code for file RDProps.h... Generating code for file RDThreads.h... Generating code for file RDValue-doublemagic.h... Generating code for file RDValue-taggedunion.h... Generating code for file RDValue.h... Generating code for file StreamOps.h... Generating code for file types.h... Generating code for file utils.h... Generating code for file versions.h... Generating code for file DistPicker.h... Generating code for file HierarchicalClusterPicker.h... Generating code for file LeaderPicker.h... Generating code for file MaxMinPicker.h... Generating file documentation... Generating docs for file Catalog.h... Generating docs for file CatalogEntry.h... Generating docs for file CatalogParams.h... Generating docs for file ChemicalFeature.h... Generating docs for file FreeChemicalFeature.h... Generating docs f/build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitOps.h:188: warning: found at different nesting level (7) than expected (4) /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitOps.h:189: warning: end of comment block while expecting command or file MetricFuncs.h... Generating docs for file MetricMatrixCalc.h... Generating docs for file base64.h... Generating docs for file BitOps.h... Generating docs for file BitVect.h... Generating docs for file BitVects.h... Generating docs for file BitVectUtils.h... Generating docs for file DatastructsException.h... Generating docs for file DatastructsStreamOps.h... Generating docs for file DiscreteDistMat.h... Generating docs for file DiscreteValueVect.h... Generating docs for file ExplicitBitVect.h... Generating docs for file FPBReader.h... Generating docs for file MultiFPBReader.h... Generating docs for file SparseBitVect.h... Generating docs for file SparseIntVect.h... Generating docs for file BoundsMatrix.h... Generating docs for file ChiralSet.h... Generating docs for file ChiralViolationContrib.h... Generating docs for file DistGeomUtils.h... Generating docs for file DistViolationContrib.h... Generating docs for file FourthDimContrib.h... Generating docs for file TriangleSmooth.h... Generating docs for file Feature.h... Generating docs for file Contrib.h... Generating docs for file ForceField.h... Generating docs for file AngleBend.h... Generating docs for file AngleBend.h... Generating docs for file AngleConstraint.h... Generating docs for file AngleConstraint.h... Generating docs for file BondStretch.h... Generating docs for file BondStretch.h... Generating docs for file Contribs.h... Generating docs for file Contribs.h... Generating docs for file DistanceConstraint.h... Generating docs for file DistanceConstraint.h... Generating docs for file Nonbonded.h... Generating docs for file Nonbonded.h... Generating docs for file OopBend.h... Generating docs for file Params.h... Generating docs for file Params.h... Generating docs for file PositionConstraint.h... Generating docs for file PositionConstraint.h... Generating docs for file StretchBend.h... Generating docs for file TorsionAngle.h... Generating docs for file TorsionAngle.h... Generating docs for file TorsionConstraint.h... Generating docs for file TorsionConstraint.h... Generating docs for file Inversion.h... Generating docs for file Grid3D.h... Generating docs for file GridUtils.h... Generating docs for file point.h... Generating docs for file Transform.h... Generating docs for file Transform2D.h... Generating docs for file Transform3D.h... Generating docs for file UniformGrid3D.h... Generating docs for file Utils.h... Generating docs for file Abbreviations.h... Generating docs for file Atom.h... Generating docs for file atomic_data.h... Generating docs for file AtomIterators.h... Generating docs for file Bond.h... Generating docs for file BondIterators.h... Generating docs for file Canon.h... Generating docs for file CartesianProduct.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 EvenSamplePairs.h... Generating docs for file RandomSample.h... Generating docs for file RandomSampleAllBBs.h... Generating docs for file PreprocessRxn.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 SanitizeRxn.h... Generating docs for file ChemTransforms.h... Generating docs for file MolFragmenter.h... Generating docs for file Chirality.h... Generating docs for file CIPLabeler.h... Generating docs for file CIPMol.h... Generating docs for file Configuration.h... Generating docs for file Sp2Bond.h... Generating docs for file Tetrahedral.h... Generating docs for file Descriptor.h... Generating docs for file Digraph.h... Generating docs for file Edge.h... Generating docs for file Mancude.h... Generating docs for file Node.h... Generating docs for file Priority.h... Generating docs for file Pairlist.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 SequenceRule.h... Generating docs for file Sort.h... Generating docs for file TooManyNodesException.h... Generating docs for file Conformer.h... Generating docs for file DepictUtils.h... Generating docs for file EmbeddedFrag.h... Generating docs for file RDDepictor.h... Generating docs for file Templates.h... Generating docs for file TemplateSmiles.h... Generating docs for file Deprotect.h... Generating docs for file AtomFeat.h... Generating docs for file AUTOCORR2D.h... Generating docs for file AUTOCORR3D.h... Generating docs for file BCUT.h... Generating docs for file ConnectivityDescriptors.h... Generating docs for file CoulombMat.h... Generating docs for file Crippen.h... Generating docs for file Data3Ddescriptors.h... Generating docs for file EEM.h... Generating docs for file GETAWAY.h... Generating docs for file Lipinski.h... Generating docs for file MolData3Ddescriptors.h... Generating docs for file MolDescriptors.h... Generating docs for file MolDescriptors3D.h... Generating docs for file MolSurf.h... Generating docs for file MORSE.h... Generating docs for file MQN.h... Generating docs for file OxidationNumbers.h... Generating docs for file PBF.h... Generating docs for file PMI.h... Generating docs for file Property.h... Generating docs for file RDF.h... Generating docs for file RegisterDescriptor.h... Generating docs for file USRDescriptor.h... Generating docs for file WHIM.h... Generating docs for file details.h... Generating docs for file details.h... Generating docs for file DetermineBonds.h... Generating docs for file BoundsMatrixBuilder.h... Generating docs for file Embedder.h... Generating docs for file CDXMLParser.h... Generating docs for file FileParsers.h... Generating docs for file FileParserUtils.h... Generating docs for file GeneralFileReader.h... Generating docs for file MolFileStereochem.h... Generating docs for file MolSGroupParsing.h... Generating docs for file MolSGroupWriting.h... Generating docs for file MolSupplier.h... Generating docs for file MolWriters.h... Generating docs for file MultithreadedMolSupplier.h... Generating docs for file MultithreadedSDMolSupplier.h... Generating docs for file MultithreadedSmilesMolSupplier.h... Generating docs for file PNGParser.h... Generating docs for file ProximityBonds.h... Generating docs for file SequenceParsers.h... Generating docs for file SequenceWriters.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 FunctionalGroupHierarchy.h... Generating docs for file AtomPairGenerator.h... Generating docs for file AtomPairs.h... Generating docs for file FingerprintGenerator.h... Generating docs for file Fingerprints.h... Generating docs for file FingerprintUtil.h... Generating docs for file MACCS.h... Generating docs for file MHFP.h... Generating docs for file MorganFingerprints.h... Generating docs for file MorganGenerator.h... Generating docs for file RDKitFPGenerator.h... Generating docs for file TopologicalTorsionGenerator.h... Generating docs for file Composition2N.h... Generating docs for file DebugTrace.h... Generating docs for file DuplicatedSeedCache.h... Generating docs for file FMCS.h... Generating docs for file Graph.h... Generating docs for file MatchTable.h... Generating docs for file MaximumCommonSubgraph.h... Generating docs for file Seed.h... Generating docs for file SeedSet.h... Generating docs for file SubstructMatchCustom.h... Generating docs for file SubstructureCache.h... Generating docs for file Target.h... Generating docs for file TargetMatch.h... Generating docs for file TorsionAngleM6.h... Generating docs for file TorsionPreferences.h... Generating docs for file FFConvenience.h... Generating docs for file AtomTyper.h... Generating docs for file AtomTyper.h... Generating docs for file Builder.h... Generating docs for file Builder.h... Generating docs for file MMFF.h... Generating docs for file UFF.h... Generating docs for file FragCatalogEntry.h... Generating docs for file FragCatalogUtils.h... Generating docs for file FragCatGenerator.h... Generating docs for file FragCatParams.h... Generating docs for file FragFPGenerator.h... Generating docs for file XQMol.h... Generating docs for file GenericGroups.h... Generating docs for file GraphMol.h... Generating docs for file MarvinDefs.h... Generating docs for file MarvinParser.h... Generating docs for file MMPA.h... Generating docs for file AlignMolecules.h... Generating docs for file O3AAlignMolecules.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 FeatureParser.h... Generating docs for file MolChemicalFeature.h... Generating docs for file MolChemicalFeatureDef.h... Generating docs for file MolChemicalFeatureFactory.h... Generating docs for file AtomSymbol.h... Generating docs for file DrawAnnotation.h... Generating docs for file DrawMol.h... Generating docs for file DrawMolMCH.h... Generating docs for file DrawMolMCHCircleAndLine.h... Generating docs for file DrawMolMCHLasso.h... Generating docs for file DrawShape.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 DrawTextFTSVG.h... Generating docs for file DrawTextJS.h... Generating docs for file DrawTextNotFT.h... Generating docs for file DrawTextSVG.h... Generating docs for file roboto_regular.h... Generating docs for file telex_regular.h... Generating docs for file MolDraw2D.h... Generating docs for file MolDraw2DCairo.h... Generating docs for file MolDraw2DDetails.h... Generating docs for file MolDraw2DHelpers.h... Generating docs for file MolDraw2DJS.h... 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Generating docs for file Metal.h... Generating docs for file MolStandardize.h... Generating docs for file Normalize.h... Generating docs for file Tautomer.h... Generating docs for file Tautomer.h... Generating docs for file TautomerCatalogEntry.h... Generating docs for file TautomerCatalogParams.h... Generating docs for file TautomerCatalogUtils.h... Generating docs for file TransformCatalogEntry.h... Generating docs for file TransformCatalogParams.h... Generating docs for file TransformCatalogUtils.h... Generating docs for file Validate.h... Generating docs for file MolTransforms.h... Generating docs for file MonomerInfo.h... Generating docs for file new_canon.h... Generating docs for file GasteigerCharges.h... Generating docs for file GasteigerParams.h... Generating docs for/build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:525: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:534: warning: Found unknown command '\overloadquery' file PeriodicTable.h... Generating docs for file QueryAtom.h... Generating docs for file QueryBond.h... Generating docs for file QueryOps.h... Generating docs for file PartitionSet.h... Generating docs for file RascalClusterOptions.h... Generating docs for file RascalDetails.h... Generating docs for file RascalMCES.h... Generating docs for file RascalOptions.h... Generating docs for file RascalResult.h... Generating docs for file RDKitBase.h... Generating docs for file RDKitQueries.h... Generating docs for file ReducedGraphs.h... Generating docs for file Resonance.h... Generating docs for file RGroupCore.h... Generating docs for file RGroupData.h... Generating docs for file RGroupDecomp.h... 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Generating docs for file SmilesWrite.h... Generating docs for file StereoGroup.h... Generating docs for file Pattern.h... Generating docs for file ReCharge.h... Generating docs for file Stereo.h... Generating docs for file StripSmallFragments.h... Generating docs for file StructChecker.h... Generating docs for file StructCheckerOptions.h... Generating docs for file Utilites.h... Generating docs for file Subgraphs.h... Generating docs for file SubgraphUtils.h... Generating docs for file SubstanceGroup.h... Generating docs for file SubstructMatch.h... Generating docs for file SubstructUtils.h... Generating docs for file PatternFactory.h... Generating docs for file SubstructLibrary.h... Generating docs for file SubstructLibrarySerialization.h... Generating docs for file TautomerQuery.h... Generating docs for file Snapshot.h... Generating docs for file Trajectory.h... Generating docs for file CorrMatGenerator.h... Generating docs for file InfoBitRanker.h... Generating docs for file InfoGainFuncs.h... Generating docs for file AlignPoints.h... Generating docs for file Conrec.h... Generating docs for file PowerEigenSolver.h... Generating docs for file Matrix.h... Generating docs for file BFGSOpt.h... Generating docs for file SquareMatrix.h... Generating docs for file SymmMatrix.h... Generating docs for file Vector.h... Generating docs for file AndQuery.h... Generating docs for file EqualityQuery.h... Generating docs for file GreaterEqualQuery.h... Generating docs for file GreaterQuery.h... Generating docs for file LessEqualQuery.h... Generating docs for file LessQuery.h... Generating docs for file NullQueryAlgebra.h... Generating docs for file OrQuery.h... Generating docs for file Query.h... Generating docs for file QueryObjects.h... Generating docs for file RangeQuery.h... Generating docs for file SetQuery.h... Generating docs for file XOrQuery.h... Generating docs for file boost_numpy.h... Generating docs for file import_array.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 BadFileException.h... Generating docs for file BoostEndInclude.h... Generating docs for file BoostStartInclude.h... Generating docs for file ConcurrentQueue.h... Generating docs for file Dict.h... Generating docs for file Exceptions.h... Generating docs for file export.h... G/build/reproducible-path/rdkit-202309.3/Code/DistGeom/DistGeomUtils.h:95: warning: The following parameter of DistGeom::constructForceField(const BoundsMatrix &mmat, RDGeom::PointPtrVect &positions, const VECT_CHIRALSET &csets, double weightChiral=1.0, double weightFourthDim=0.1, std::map< std::pair< int, int >, double > *extraWeights=nullptr, double basinSizeTol=5.0, boost::dynamic_bitset<> *fixedPts=nullptr) is not documented: parameter 'fixedPts' /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.h:159: warning: argument 'snapshotFreq' of command @param is not found in the argument list of ForceFields::ForceField::minimize(unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6) /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.h:159: warning: argument 'snapshotVect' of command @param is not found in the argument list of ForceFields::ForceField::minimize(unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6) /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.h:144: warning: The following parameters of ForceFields::ForceField::minimize(unsigned int snapshotFreq, RDKit::SnapshotVect *snapshotVect, unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6) are not documented: parameter 'snapshotFreq' parameter 'snapshotVect' /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleBend.h:31: warning: argument 'angleType' of command @param is not found in the argument list of ForceFields::MMFF::AngleBendContrib::AngleBendContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, const MMFFAngle *mmffAngleParams, const MMFFProp *mmffPropParamsCentralAtom) /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleBend.h:31: warning: The following parameters of ForceFields::MMFF::AngleBendContrib::AngleBendContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, const MMFFAngle *mmffAngleParams, const MMFFProp *mmffPropParamsCentralAtom) are not documented: parameter 'mmffAngleParams' parameter 'mmffPropParamsCentralAtom' /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleConstraint.h:28: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::MMFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleConstraint.h:28: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::MMFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleConstraint.h:28: warning: The following parameters of ForceFields::MMFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented: parameter 'minAngleDeg' parameter 'maxAngleDeg' /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/BondStretch.h:28: warning: argument 'bondType' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/BondStretch.h:28: warning: argument 'end1Params' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/BondStretch.h:28: warning: argument 'end2Params' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/BondStretch.h:28: warning: The following parameter of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) is not documented: parameter 'mmffBondParams' /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Nonbonded.h:54: warning: The following parameters of ForceFields::MMFF::EleContrib::EleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, double chargeTerm, std::uint8_t dielModel, bool is1_4) are not documented: parameter 'chargeTerm' parameter 'dielModel' parameter 'is1_4' enerating docs for file FileParseException.h... Generating docs for file hanoiSort.h... Generating docs for file Invariant.h... Generating docs for file LocaleSwitcher.h... Generating docs for file Ranking.h... Generating docs for file RDAny.h... Generating docs for file RDConfig.h... Generating docs for file RDExportMacros.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 StreamOps.h... Generating docs for file types.h... Generating docs for file utils.h... Generating docs for file versions.h... Generating docs for file DistPicker.h... Generating docs for file HierarchicalClusterPicker.h... Generating docs for file LeaderPicker.h... Generating docs for file MaxMinPicker.h... Generating page documentation... Generating docs for page deprecated... Generating group documentation... Generating class documentation... Generating docs for compound BitVect... Generating docs for compound Data3Ddescriptors... Generating docs for compound DatastructsException... Generating docs for compound ExplicitBitVect... Generating docs for compound IndexErrorException... Generating docs for compound KeyErrorException... Generating docs for compound MolData3Ddescriptors... Generating docs for compound PySequenceHolder... Generating docs for compound SparseBitVect... Generating docs for compound ValueErrorException... Generating concept documentation... Generating module documentation... Generating namespace documentation... 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::ostream... 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 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 compound conrec::tplHash... 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::ForceField... Generating docs for compound ForceFields::ForceFieldContrib... Generating docs for namespace ForceFields::CrystalFF Generating docs for compound ForceFields::CrystalFF::CrystalFFDetails... Generating docs for compound ForceFields::CrystalFF::ExpTorsionAngle... Generating docs for compound ForceFields::CrystalFF::TorsionAngleContribM6... 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::EleContrib... Generating docs for compound ForceFields::MMFF::MMFFAngle... Generating docs for compound ForceFields::MMFF::MMFFAngleCollection... Generating docs for compound ForceFields::MMFF::MMFFAromCollection... Generating docs for compound ForceFields::MMFF::MMFFBndkCollection... Generating docs for compound ForceField/build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/PositionConstraint.h:29: warning: argument 'minDispl' of command @param is not found in the argument list of ForceFields::MMFF::PositionConstraintContrib::PositionConstraintContrib(ForceField *owner, unsigned int idx, double maxDispl, double forceConst) /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/StretchBend.h:32: warning: argument 'angleType' of command @param is not found in the argument list of ForceFields::MMFF::StretchBendContrib::StretchBendContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const MMFFStbn *mmffStbnParams, const MMFFAngle *mmffAngleParams, const MMFFBond *mmffBondParams1, const MMFFBond *mmffBondParams2) /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/StretchBend.h:32: warning: The following parameters of ForceFields::MMFF::StretchBendContrib::StretchBendContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const MMFFStbn *mmffStbnParams, const MMFFAngle *mmffAngleParams, const MMFFBond *mmffBondParams1, const MMFFBond *mmffBondParams2) are not documented: parameter 'mmffStbnParams' parameter 'mmffAngleParams' parameter 'mmffBondParams1' parameter 'mmffBondParams2' /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionAngle.h:31: 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-202309.3/Code/ForceField/MMFF/TorsionAngle.h:31: 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-202309.3/Code/ForceField/MMFF/Nonbonded.h:30: warning: The following parameter of ForceFields::MMFF::VdWContrib::VdWContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, const MMFFVdWRijstarEps *mmffVdWConstants) is not documented: parameter 'mmffVdWConstants' /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleConstraint.h:28: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::UFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleConstraint.h:28: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::UFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleConstraint.h:28: warning: The following parameters of ForceFields::UFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented: parameter 'minAngleDeg' parameter 'maxAngleDeg' /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Inversion.h:27: 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-202309.3/Code/ForceField/UFF/PositionConstraint.h:29: warning: argument 'minDispl' of command @param is not found in the argument list of ForceFields::UFF::PositionConstraintContrib::PositionConstraintContrib(ForceField *owner, unsigned int idx, double maxDispl, double forceConst) s::MMFF::MMFFBond... Generating docs for compound ForceFields::MMFF::MMFFBondCollection... Generating docs for compound ForceFields::MMFF::MMFFChg... Generating docs for compound ForceFields::MMFF::MMFFChgCollection... Generating docs for compound ForceFields::MMFF::MMFFCovRadPauEle... Generating docs for compound ForceFields::MMFF::MMFFCovRadPauEleCollection... Generating docs for compound ForceFields::MMFF::MMFFDef... Generating docs for compound ForceFields::MMFF::MMFFDefCollection... Generating docs for compound ForceFields::MMFF::MMFFDfsbCollection... Generating docs for compound ForceFields::MMFF::MMFFHerschbachLaurie... Generating docs for compound ForceFields::MMFF::MMFFHerschbachLaurieCollection... Generating docs for compound ForceFields::MMFF::MMFFOop... Generating docs for compound ForceFields::MMFF::MMFFOopCollection... Generating docs for compound ForceFields::MMFF::MMFFPBCI... Generating docs for compound ForceFields::MMFF::MMFFPBCICollection... Generating docs for compound ForceFields::MMFF::MMFFProp... Generating docs for compound ForceFields::MMFF::MMFFPropCollection... Generating docs for compound ForceFields::MMFF::MMFFStbn... Generating docs for compound ForceFields::MMFF::MMFFStbnCollection... Generating docs for compound ForceFields::MMFF::MMFFTor... Generating docs for compound ForceFields::MMFF::MMFFTorCollection... Generating docs for compound ForceFields::MMFF::MMFFVdW... Generating docs for compound ForceFields::MMFF::MMFFVdWCollection... Generating docs for compound ForceFields::MMFF::MMFFVdWRijstarEps... Generating docs for compound ForceFields::MMFF::OopBendContrib... Generating docs for compound ForceFields::MMFF::PositionConstraintContrib... Generating docs for compound ForceFields::MMFF::StretchBendContrib... Generating docs for compound ForceFields::MMFF::TorsionAngleContrib... Generating docs for compound ForceFields::MMFF::TorsionConstraintContrib... Generating docs for compound ForceFields::MMFF::VdWContrib... Generating docs for namespace ForceFields::MMFF::Utils Generating docs for namespace ForceFields::UFF Generating docs for compound ForceFields::UFF::AngleBendContrib... Generating docs for compound ForceFields::UFF::AngleConstraintContrib... Generating docs for compound ForceFields::UFF::AtomicParams... Generating docs for compound ForceFields::UFF::BondStretchContrib... Generating docs for compound ForceFields::UFF::DistanceConstraintContrib... Generating docs for compound ForceFields::UFF::InversionContrib... Generating docs for compound ForceFields::UFF::ParamCollection... Generating docs for compound ForceFields::UFF::PositionConstraintContrib... Generating docs for compound ForceFields::UFF::TorsionAngleContrib... Generating docs for compound ForceFields::UFF::TorsionConstraintContrib... Generating docs for compound ForceFields::UFF::UFFAngle... Generating docs for compound ForceFields::UFF::UFFBond... Generating docs for compound ForceFields::UFF::UFFInv... Generating docs for compound ForceFields::UFF::UFFTor... Generating docs for compound ForceFields::UFF::UFFVdW... Generating docs for compound ForceFields::UFF::vdWContrib... Generating docs for namespace ForceFields::UFF::Params Generating docs for namespace ForceFields::UFF::Utils Generating docs for namespace Invar Generating docs for compound Invar::Invariant... Generating docs for namespace MolTransforms Generating docs for namespace Queries Generating docs for compound Queries::AndQuery... Generating docs for compound Queries::EqualityQuery... Generating docs for compound Queries::GreaterEqualQuery... Generating docs for compound Queries::GreaterQuery... Generating docs for compound Queries::Int2Type... Generating docs for compound Queries::LessEqualQuery... Generating docs for compound Queries::LessQuery... Generating docs for compound Queries::OrQuery... Generating docs for compound Queries::Query... Generating docs for compound Queries::RangeQuery... Generating docs for compound Queries::SetQuery... Generating docs for compound Queries::XOrQuery... Generating docs for namespace Rankers Generating docs for name/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.h:393: 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-202309.3/Code/GraphMol/Depictor/RDDepictor.h:393: warning: The following parameter of RDDepict::generateDepictionMatching3DStructure(RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=nullptr, bool acceptFailure=false, bool forceRDKit=false) is not documented: parameter 'referencePattern' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:525: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:534: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstanceGroup.h:267: warning: The following parameter of RDKit::addSubstanceGroup(ROMol &mol, SubstanceGroup sgroup) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/CDXMLParser.h:42: warning: argument 'fileName' of command @param is not found in the argument list of RDKit::CDXMLFileToMols(const std::string &filename, bool sanitize=true, bool removeHs=true) /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/CDXMLParser.h:42: warning: The following parameter of RDKit::CDXMLFileToMols(const std::string &filename, bool sanitize=true, bool removeHs=true) is not documented: parameter 'filename' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceParsers.h:105: warning: argument 'seq' of command @param is not found in the argument list of RDKit::HELMToMol(const char *helm, bool sanitize=true) /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceParsers.h:105: warning: The following parameter of RDKit::HELMToMol(const char *helm, bool sanitize=true) is not documented: parameter 'helm' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Fingerprints.h:69: warning: The following parameter of RDKit::LayeredFingerprintMol(const ROMol &mol, unsigned int layerFlags=0xFFFFFFFF, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=nullptr, ExplicitBitVect *setOnlyBits=nullptr, bool branchedPaths=true, const std::vector< std::uint32_t > *fromAtoms=nullptr) is not documented: parameter 'fromAtoms' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:525: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:534: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/FileParsers.h:51: warning: argument 'line' from the argument list of RDKit::MolDataStreamToMol has multiple @param documentation sections /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.h:167: 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-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.h:216: 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-202309.3/Code/GraphMol/FileParsers/FileParsers.h:341: warning: argument 'fName' of command @param is not found in the argument list of RDKit::MolToPDBFile(const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0) /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/FileParsers.h:341: warning: The following parameter of RDKit::MolToPDBFile(const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0) is not documented: parameter 'fname' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.h:107: 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-202309.3/Code/GraphMol/Fingerprints/Fingerprints.h:120: warning: The following parameter of RDKit::PatternFingerprintMol(const ROMol &mol, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=nullptr, ExplicitBitVect *setOnlyBits=nullptr, bool tautomericFingerprint=false) is not documented: parameter 'tautomericFingerprint' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Fingerprints.h:27: warning: argument 'useBondOrders' of command @param is not found in the argument list of RDKit::RDKFingerprintMol(const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=true, bool useBondOrder=true, std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *fromAtoms=nullptr, std::vector< std::vector< std::uint32_t > > *atomBits=nullptr, std::map< std::uint32_t, std::vector< std::vector< int > > > *bitInfo=nullptr) /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Fingerprints.h:27: warning: The following parameters of RDKit::RDKFingerprintMol(const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=true, bool useBondOrder=true, std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *fromAtoms=nullptr, std::vector< std::vector< std::uint32_t > > *atomBits=nullptr, std::map< std::uint32_t, std::vector< std::vector< int > > > *bitInfo=nullptr) are not documented: parameter 'useBondOrder' parameter 'bitInfo' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionRunner.h:94: warning: The following parameter of RDKit::reduceProductToSideChains(const ROMOL_SPTR &product, bool addDummyAtoms=true) is not documented: parameter 'product' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/ChemTransforms.h:114: warning: argument 'useChirality' of command @param is not found in the argument list of RDKit::replaceCore(const ROMol &mol, const ROMol &core, const MatchVectType &matchVect, bool replaceDummies=true, bool labelByIndex=false, bool requireDummyMatch=false) /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionRunner.h:66: warning: argument 'reactantTemplateIdx' of command @param is not found in the argument list of RDKit::run_Reactant(const ChemicalReaction &rxn, const ROMOL_SPTR &reactant, unsigned int reactantIdx) /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionRunner.h:66: warning: The following parameters of RDKit::run_Reactant(const ChemicalReaction &rxn, const ROMOL_SPTR &reactant, unsigned int reactantIdx) are not documented: parameter 'rxn' parameter 'reactantIdx' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructMatch.h:81: 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-202309.3/Code/GraphMol/Substruct/SubstructMatch.h:81: 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-202309.3/Code/GraphMol/Substruct/SubstructMatch.h:94: 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-202309.3/Code/GraphMol/Substruct/SubstructMatch.h:94: 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-202309.3/Code/GraphMol/Substruct/SubstructMatch.h:149: 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-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::AtomEnvironment::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const=0 are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.h:219: 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-202309.3/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' space RDCatalog Generating docs for compound RDCatalog::Catalog... Generating docs for compound RDCatalog::CatalogEntry... Generating docs for compound RDCatalog::CatalogParams... Generating docs for compound RDCatalog::HierarchCatalog... Generating docs for nested compound RDCatalog::HierarchCatalog::vertex_entry_t... Generating docs for namespace RDDataManip Generating docs for compound RDDataManip::MetricMatrixCalc... Generating docs for namespace RDDepict Generating docs for compound RDDepict::Compute2DCoordParameters... Generating docs for compound RDDepict::ConstrainedDepictionParams... Generating docs for compound RDDepict::CoordinateTemplates... Generating docs for compound RDDepict::DepictException... Generating docs for compound RDDepict::EmbeddedAtom... Generating docs for compound RDDepict::EmbeddedFrag... Generating docs for compound RDDepict::gtIIPair... Generating docs for namespace RDFeatures Generating docs for compound RDFeatures::ExplicitFeature... Generating docs for compound RDFeatures::ImplicitFeature... Generating docs for namespace RDGeom Generating docs for compound RDGeom::Grid3D... Generating docs for compound RDGeom::GridException... Generating docs for compound RDGeom::Point... Generating docs for compound RDGeom::Point2D... Generating docs for compound RDGeom::Point3D... Generating docs for compound RDGeom::PointND... Generating docs for compound RDGeom::Transform2D... Generating docs for compound RDGeom::Transform3D... Generating docs for compound RDGeom::UniformGrid3D... Generating docs for namespace RDInfoTheory Generating docs for compound RDInfoTheory::BitCorrMatGenerator... Generating docs for compound RDInfoTheory::InfoBitRanker... Generating docs for namespace RDKit Generating docs for compound RDKit::AdditionalOutput... Generating docs for compound RDKit::AromaticAtomIterator_... Generating docs for compound RDKit::Atom... Generating docs for compound RDKit::AtomEnvironment... Generating docs for compound RDKit::AtomEnvironmentGenerator... Generating docs for compound RDKit::atomicData... Generating docs for compound RDKit::AtomInvariantsGenerator... Generating docs for compound RDKit::AtomIterator_... Generating docs for compound RDKit::AtomKekulizeException... Generating docs for compound RDKit::AtomMonomerInfo... Generating docs for compound RDKit::AtomPDBResidueInfo... Generating docs for compound RDKit::AtomRingQuery... Generating docs for compound RDKit::AtomSanitizeException... Generating docs for compound RDKit::AtomValenceException... Generating docs for compound RDKit::BadFileException... Generating docs for compound RDKit::Bond... Generating docs for compound RDKit::BondInvariantsGenerator... Generating docs for compound RDKit::BondIterator_... Generating docs for compound RDKit::CachedMolHolder... Generating docs for compound RDKit::CachedSmilesMolHolder... Generating docs for compound RDKit::CachedTrustedSmilesMolHolder... Generating docs for compound RDKit::CartesianProduct... Generating docs for compound RDKit::CartesianProductStrategy... Generating docs for compound RDKit::charptr_functor... Generating docs for compound RDKit::ChemicalReaction... Generating docs for compound RDKit::ChemicalReactionException... Generating docs for compound RDKit::ChemicalReactionParserException... Generating docs for compound RDKit::Conformer... Generating docs for compound RDKit::ConformerException... Generating docs for compound RDKit::ConstBondIterator_... Generating docs for compound RDKit::CustomPropHandler... Generating docs for compound RDKit::CXXAtomIterator... Generating docs for nested compound RDKit::CXXAtomIterator::CXXAtomIter... Generating docs for compound RDKit::CXXBondIterator... Generating docs for nested compound RDKit::CXXBondIterator::CXXBondIter... Generating docs for compound RDKit::DataStructsExplicitBitVecPropHandler... Generating docs for compound RDKit::Dict... Generating docs for nested compound RDKit::Dict::Pair... Generating docs for compound RDKit::DiscreteDistMat... Generating docs for compound RDKit::DiscreteValueVect... Generating docs for compound RD/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatchers.h:430: warning: argument 'matches' of command @param is not found in the argument list of RDKit::ExclusionList::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 101 in file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: The following parameter of RDKit::ExclusionList::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatcherBase::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const=0 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: The following parameter of RDKit::FilterMatcherBase::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const=0 is not documented: parameter 'matchVect' Kit::DrawColour... Generating docs for compound RDKit::EnumerateLibrary... Generating docs for compound RDKit::EnumerateLibraryBase... Generating docs for compound RDKit::EnumerationParams... Generating docs for compound RDKit::EnumerationStrategyBase... Generating docs for compound RDKit::EnumerationStrategyException... Generating docs for compound RDKit::EvenSamplePairsStrategy... Generating docs for compound RDKit::ExclusionList... Generating docs for compound RDKit::FeatureFileParseException... Generating docs for compound RDKit::FileParseException... Generating docs for compound RDKit::FilterCatalog... Generating docs for compound RDKit::FilterCatalogEntry... Generating docs for compound RDKit::FilterCatalogParams... Generating docs for compound RDKit::FilterData_t... Generating docs for compound RDKit::FilterHierarchyMatcher... Generating docs for compound RDKit::FilterMatch... Generating docs for compound RDKit::FilterMatcherBase... Generating docs for compound RDKit::FilterProperty_t... Generating docs for compound RDKit::FingerprintArguments... Generating docs for compound RDKit::FingerprintFuncArguments... Generating docs for compound RDKit::FingerprintGenerator... Generating docs for compound RDKit::FingerprintVarianceScoreData... Generating docs for compound RDKit::FixedMolSizeMolBundle... Generating docs for compound RDKit::ForwardSDMolSupplier... Generating docs for compound RDKit::FPBReader... Generating docs for compound RDKit::FPHolderBase... Generating docs for compound RDKit::FragCatalogEntry... Generating docs for compound RDKit::FragCatGenerator... Generating docs for compound RDKit::FragCatParams... Generating docs for compound RDKit::FragFPGenerator... Generating docs for compound RDKit::GaResult... Generating docs for compound RDKit::GasteigerParams... Generating docs for compound RDKit::HasPropQuery... Generating docs for compound RDKit::HasPropWithValueQuery... Generating docs for compound RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect >... Generating docs for compound RDKit::HasPropWithValueQuery< TargetPtr, std::string >... Generating docs for compound RDKit::HeteroatomIterator_... Generating docs for compound RDKit::KekulizeException... Generating docs for compound RDKit::KeyFromPropHolder... Generating docs for compound RDKit::KeyHolderBase... Generating docs for compound RDKit::larger_of... Generating docs for compound RDKit::ltDouble... Generating docs for compound RDKit::MarvinArrow... Generating docs for compound RDKit::MarvinAtom... Generating docs for compound RDKit::MarvinAttachmentPoint... Generating docs for compound RDKit::MarvinBond... Generating docs for compound RDKit::MarvinBondStereo... Generating docs for compound RDKit::MarvinCondition... Generating docs for compound RDKit::MarvinDataSgroup... Generating docs for compound RDKit::MarvinGenericSgroup... Generating docs for compound RDKit::MarvinMol... Generating docs for compound RDKit::MarvinMolBase... Generating docs for compound RDKit::MarvinMonomerSgroup... Generating docs for compound RDKit::MarvinMulticenterSgroup... Generating docs for compound RDKit::MarvinMultipleSgroup... Generating docs for compound RDKit::MarvinPlus... Generating docs for compound RDKit::MarvinReaction... Generating docs for compound RDKit::MarvinRectangle... Generating docs for compound RDKit::MarvinSruCoModSgroup... Generating docs for compound RDKit::MarvinStereoGroup... Generating docs for compound RDKit::MarvinSuperatomSgroup... Generating docs for compound RDKit::MarvinSuperatomSgroupExpanded... Generating docs for compound RDKit::MarvinWriterException... Generating docs for compound RDKit::MatchingAtomIterator_... Generating docs for compound RDKit::MCSAtomCompareParameters... Generating docs for compound RDKit::MCSBondCompareParameters... Generating docs for compound RDKit::MCSParameters... Generating docs for compound RDKit::MCSProgressData... Generating docs for compound RDKit::MCSResult... Generating docs for compound RDKit::MolBundle... Generating docs for compound RDKit::MolCatalogEntry... Generating docs for compound RDKit::/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:71: warning: argument 'highlight_atoms' from the argument list of RDKit::MolDraw2D::drawMolecule has multiple @param documentation sections /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:71: warning: The following parameter of RDKit::MolDraw2D::drawMolecule(const ROMol &mol, const std::string &legend, const std::vector< int > *highlight_atoms, const std::vector< int > *highlight_bonds, const std::map< int, DrawColour > *highlight_atom_map=nullptr, const std::map< int, DrawColour > *highlight_bond_map=nullptr, const std::map< int, double > *highlight_radii=nullptr, int confId=-1) is not documented: parameter 'highlight_bonds' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: 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-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: 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-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: 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-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: warning: argument 'highlight_atoms' from the argument list of RDKit::MolDraw2D::drawMolecules has multiple @param documentation sections /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: 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-202309.3/Code/GraphMol/Resonance.h:114: warning: argument 'numThreads' of command @param is not found in the argument list of RDKit::ResonanceMolSupplier::ResonanceMolSupplier(ROMol &mol, unsigned int flags=0, unsigned int maxStructs=1000) /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatchers.h:336: warning: argument 'matches' of command @param is not found in the argument list of RDKit::SmartsMatcher::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 101 in file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: The following parameter of RDKit::SmartsMatcher::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' MolCatalogParams... Generating docs for compound RDKit::MolChemicalFeature... Generating docs for compound RDKit::MolChemicalFeatureDef... Generating docs for compound RDKit::MolChemicalFeatureFactory... Generating docs for compound RDKit::MolDraw2D... Generating docs for compound RDKit::MolDraw2DCairo... Generating docs for compound RDKit::MolDraw2DJS... Generating docs for compound RDKit::MolDraw2DQt... Generating docs for compound RDKit::MolDraw2DSVG... Generating docs for compound RDKit::MolDraw2Dwx... Generating docs for compound RDKit::MolDrawOptions... Generating docs for compound RDKit::MolFileUnhandledFeatureException... Generating docs for compound RDKit::MolHolder... Generating docs for compound RDKit::MolHolderBase... Generating docs for compound RDKit::MolMatchFinalCheckFunctor... Generating docs for compound RDKit::MolPickler... Generating docs for compound RDKit::MolPicklerException... Generating docs for compound RDKit::MolSanitizeException... Generating docs for compound RDKit::MolSupplier... Generating docs for compound RDKit::MolWriter... Generating docs for compound RDKit::MolzipParams... Generating docs for compound RDKit::MultiFPBReader... Generating docs for compound RDKit::PatternHolder... Generating docs for compound RDKit::PDBMolSupplier... Generating docs for compound RDKit::PDBWriter... Generating docs for compound RDKit::PeriodicTable... Generating docs for compound RDKit::QueryAtom... Generating docs for compound RDKit::QueryAtomIterator_... Generating docs for compound RDKit::QueryBond... Generating docs for compound RDKit::RandomSampleAllBBsStrategy... Generating docs for compound RDKit::RandomSampleStrategy... Generating docs for compound RDKit::RCore... Generating docs for compound RDKit::RDAny... Generating docs for compound RDKit::RDProps... Generating docs for compound RDKit::RDValue... Generating docs for compound RDKit::ReactionFingerprintParams... Generating docs for compound RDKit::ReactionPickler... Generating docs for compound RDKit::ReactionPicklerException... Generating docs for compound RDKit::RecursiveStructureQuery... Generating docs for compound RDKit::ResonanceMolSupplier... Generating docs for compound RDKit::ResonanceMolSupplierCallback... Generating docs for compound RDKit::RGroupData... Generating docs for compound RDKit::RGroupDecompData... Generating docs for nested compound RDKit::RGroupDecompData::UsedLabels... Generating docs for compound RDKit::RGroupDecomposition... Generating docs for compound RDKit::RGroupDecompositionChromosome... Generating docs for compound RDKit::RGroupDecompositionParameters... Generating docs for compound RDKit::RGroupDecompositionProcessResult... Generating docs for compound RDKit::RGroupGa... Generating docs for compound RDKit::RGroupMatch... Generating docs for compound RDKit::RGroupScorer... Generating docs for compound RDKit::RingInfo... Generating docs for compound RDKit::ROMol... Generating docs for compound RDKit::RWMol... Generating docs for compound RDKit::RxnSanitizeException... Generating docs for compound RDKit::SDMolSupplier... Generating docs for compound RDKit::SDWriter... Generating docs for compound RDKit::SLNParseException... Generating docs for compound RDKit::SmartsMatcher... Generating docs for compound RDKit::SmartsParserParams... Generating docs for compound RDKit::SmilesMolSupplier... Generating docs for compound RDKit::SmilesParseException... Generating docs for compound RDKit::SmilesParserParams... Generating docs for compound RDKit::SmilesWriteParams... Generating docs for compound RDKit::SmilesWriter... Generating docs for compound RDKit::Snapshot... Generating docs for compound RDKit::SparseIntVect... Generating docs for compound RDKit::StereoBondThresholds... Generating docs for compound RDKit::StereoGroup... Generating docs for compound RDKit::SubstanceGroup... Generating docs for nested compound RDKit::SubstanceGroup::AttachPoint... Generating docs for nested compound RDKit::SubstanceGroup::CState... Generating docs for compound RDKit::SubstanceGroupException... Generating docs for compound RDKit::Substr/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Abbreviations.h:104: warning: The following parameter of RDKit::Abbreviations::findApplicableAbbreviationMatches(const ROMol &mol, const std::vector< AbbreviationDefinition > &abbrevs, double maxCoverage=0.4) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::AtomPair::AtomPairAtomEnv::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairs.h:95: warning: The following parameter of RDKit::AtomPairs::getHashedAtomPairFingerprint(const ROMol &mol, unsigned int nBits=2048, unsigned int minLength=1, unsigned int maxLength=maxPathLen - 1, const std::vector< std::uint32_t > *fromAtoms=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const std::vector< std::uint32_t > *atomInvariants=nullptr, bool includeChirality=false, bool use2D=true, int confId=-1) is not documented: parameter 'confId' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintUtil.h:75: warning: The following parameter of RDKit::AtomPairs::getTopologicalTorsionCode(const std::vector< std::uint32_t > &atomCodes, bool includeChirality=false) is not documented: parameter 'includeChirality' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Canon.h:103: warning: The following parameters of RDKit::Canon::canonicalizeFragment(ROMol &mol, int atomIdx, std::vector< AtomColors > &colors, const std::vector< unsigned int > &ranks, MolStack &molStack, const boost::dynamic_bitset<> *bondsInPlay=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=false, bool doRandom=false, bool doChiralInversions=true) are not documented: parameter 'bondsInPlay' parameter 'bondSymbols' parameter 'doIsomericSmiles' parameter 'doRandom' parameter 'doChiralInversions' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.h:138: warning: The following parameter of RDKit::Chirality::findPotentialStereo(ROMol &mol, bool cleanIt, bool flagPossible=true) is not documented: parameter 'flagPossible' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.h:190: warning: The following parameter of RDKit::Chirality::getTrigonalBipyramidalAxialBond(const Atom *center, int which=0) is not documented: parameter 'center' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPLabeler.h:44: warning: The following parameter of RDKit::CIPLabeler::assignCIPLabels(ROMol &mol, unsigned int maxRecursiveIterations=0) is not documented: parameter 'maxRecursiveIterations' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Lipinski.h:45: warning: argument 'strict' of command @param is not found in the argument list of RDKit::Descriptors::calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default) /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Lipinski.h:45: warning: The following parameter of RDKit::Descriptors::calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default) is not documented: parameter 'useStrictDefinition' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/USRDescriptor.h:68: warning: The following parameter of RDKit::Descriptors::USRCAT(const ROMol &mol, std::vector< double > &descriptor, std::vector< std::vector< unsigned int > > &atomIds, int confId=-1) is not documented: parameter 'atomIds' uctLibrary... Generating docs for compound RDKit::SubstructMatchParameters... Generating docs for compound RDKit::TautomerPatternHolder... Generating docs for compound RDKit::TautomerQuery... Generating docs for compound RDKit::TDTMolSupplier... Generating docs for compound RDKit::TDTWriter... Generating docs for compound RDKit::Trajectory... Generating docs for compound RDKit::UnimplementedFPException... Generating docs for compound RDKit::UsedLabelMap... Generating docs for compound RDKit::VarianceDataForLabel... Generating docs for namespace RDKit::Abbreviations Generating docs for compound RDKit::Abbreviations::AbbreviationDefinition... Generating docs for compound RDKit::Abbreviations::AbbreviationMatch... Generating docs for namespace RDKit::Abbreviations::common_properties Generating docs for namespace RDKit::Abbreviations::Utils Generating docs for namespace RDKit::AtomPair Generating docs for compound RDKit::AtomPair::AtomPairArguments... Generating docs for compound RDKit::AtomPair::AtomPairAtomEnv... Generating docs for compound RDKit::AtomPair::AtomPairAtomInvGenerator... Generating docs for compound RDKit::AtomPair::AtomPairEnvGenerator... Generating docs for namespace RDKit::AtomPairs Generating docs for namespace RDKit::Canon Generating docs for compound RDKit::Canon::AtomCompareFunctor... Generating docs for compound RDKit::Canon::bondholder... Generating docs for compound RDKit::Canon::canon_atom... Generating docs for compound RDKit::Canon::ChiralAtomCompareFunctor... Generating docs for compound RDKit::Canon::MolStackElem... Generating docs for compound RDKit::Canon::MolStackUnion... Generating docs for compound RDKit::Canon::SpecialChiralityAtomCompareFunctor... Generating docs for compound RDKit::Canon::SpecialSymmetryAtomCompareFunctor... Generating docs for namespace RDKit::Canon::detail Generating docs for namespace RDKit::Chirality Generating docs for compound RDKit::Chirality::BondWedgingParameters... Generating docs for compound RDKit::Chirality::StereoInfo... Generating docs for namespace RDKit::Chirality::detail Generating docs for namespace RDKit::CIPLabeler Generating docs for compound RDKit::CIPLabeler::CIPMol... Generating docs for compound RDKit::CIPLabeler::CIPMolSpan... Generating docs for nested compound RDKit::CIPLabeler::CIPMolSpan::CIPMolIter... Generating docs for compound RDKit::CIPLabeler::Configuration... Generating docs for compound RDKit::CIPLabeler::Digraph... Generating docs for compound RDKit::CIPLabeler::Edge... Generating docs for compound RDKit::CIPLabeler::MaxIterationsExceeded... Generating docs for compound RDKit::CIPLabeler::Node... Generating docs for compound RDKit::CIPLabeler::PairList... Generating docs for compound RDKit::CIPLabeler::Priority... Generating docs for compound RDKit::CIPLabeler::Rule1a... Generating docs for compound RDKit::CIPLabeler::Rule1b... Generating docs for compound RDKit::CIPLabeler::Rule2... Generating docs for compound RDKit::CIPLabeler::Rule3... Generating docs for compound RDKit::CIPLabeler::Rule4a... Generating docs for compound RDKit::CIPLabeler::Rule4b... Generating docs for compound RDKit::CIPLabeler::Rule4c... Generating docs for compound RDKit::CIPLabeler::Rule5... Generating docs for compound RDKit::CIPLabeler::Rule5New... Generating docs for compound RDKit::CIPLabeler::Rule6... Generating docs for compound RDKit::CIPLabeler::Rules... Generating docs for compound RDKit::CIPLabeler::SequenceRule... Generating docs for compound RDKit::CIPLabeler::Sort... Generating docs for compound RDKit::CIPLabeler::Sp2Bond... Generating docs for compound RDKit::CIPLabeler::Tetrahedral... Generating docs for compound RDKit::CIPLabeler::TooManyNodesException... Generating docs for namespace RDKit::CIPLabeler_detail Generating docs for namespace RDKit::common_properties Generating docs for namespace RDKit::constants Generating docs for namespace RDKit::Deprotect Generating docs for compound RDKit::Deprotect::DeprotectData... Generating docs for namespace RDKit::Descriptors Generating docs for compound RDKit::Descriptors::CrippenParamCollection.../build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h:37: warning: The following parameter of RDKit::DGeomHelpers::setTopolBounds(const ROMol &mol, DistGeom::BoundsMatPtr mmat, bool set15bounds=true, bool scaleVDW=false, bool useMacrocycle14config=false, bool forceTransAmides=true) is not documented: parameter 'forceTransAmides' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatchers.h:98: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::And::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 101 in file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: The following parameter of RDKit::FilterMatchOps::And::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatchers.h:218: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::Not::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 101 in file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: The following parameter of RDKit::FilterMatchOps::Not::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatchers.h:161: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 101 in file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: The following parameter of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MHFP.h:102: warning: found tag without matching /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MHFP.h:93: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::CreateShingling(const ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=false, unsigned char min_radius=1) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MHFP.h:141: warning: found tag without matching /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MHFP.h:132: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::Encode(ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=false, unsigned char min_radius=1) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MHFP.h:191: warning: found tag without matching /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MHFP.h:183: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::EncodeSECFP(ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=false, unsigned char min_radius=1, size_t length=2048) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/MMPA.h:23: warning: The following parameter of RDKit::MMPA::fragmentMol(const ROMol &mol, std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > &result, unsigned int maxCuts=3, unsigned int maxCutBonds=20, const std::string &pattern="[#6+0;!$(*=,#[!#6])]!@!=!#[*]") is not documented: parameter 'pattern' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/MMPA.h:44: warning: The following parameter of RDKit::MMPA::fragmentMol(const ROMol &mol, std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > &result, unsigned int minCuts, unsigned int maxCuts, unsigned int maxCutBonds, const std::string &pattern="[#6+0;!$(*=,#[!#6])]!@!=!#[*]") is not documented: parameter 'pattern' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/AlignMolecules.h:148: warning: argument 'trans' of command @param is not found in the argument list of RDKit::MolAlign::getBestRMS(ROMol &prbMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, bool symmetrizeConjugatedTerminalGroups=true, const RDNumeric::DoubleVector *weights=nullptr, int numThreads=1) /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/AtomSymbol.h:38: warning: The following parameters of RDKit::MolDraw2D_detail::AtomSymbol::AtomSymbol(const std::string &symbol, int atIdx, OrientType orient, const Point2D &cds, const DrawColour &colour, DrawText &textDrawer) are not documented: parameter 'atIdx' parameter 'cds' parameter 'colour' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.h:45: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMol::DrawMol(const ROMol &mol, const std::string &legend, int width, int height, const MolDrawOptions &drawOptions, DrawText &textDrawer, const std::vector< int > *highlightAtoms=nullptr, const std::vector< int > *highlightBonds=nullptr, const std::map< int, DrawColour > *highlightAtomMap=nullptr, const std::map< int, DrawColour > *highlightBondMap=nullptr, const std::vector< std::pair< DrawColour, DrawColour > > *bondColours=nullptr, const std::map< int, double > *highlight_radii=nullptr, bool includeAnnotations=true, int confId=-1, bool isReactionMol=false) /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.h:45: warning: The following parameters of RDKit::MolDraw2D_detail::DrawMol::DrawMol(const ROMol &mol, const std::string &legend, int width, int height, const MolDrawOptions &drawOptions, DrawText &textDrawer, const std::vector< int > *highlightAtoms=nullptr, const std::vector< int > *highlightBonds=nullptr, const std::map< int, DrawColour > *highlightAtomMap=nullptr, const std::map< int, DrawColour > *highlightBondMap=nullptr, const std::vector< std::pair< DrawColour, DrawColour > > *bondColours=nullptr, const std::map< int, double > *highlight_radii=nullptr, bool includeAnnotations=true, int confId=-1, bool isReactionMol=false) are not documented: parameter 'bondColours' parameter 'highlight_radii' parameter 'includeAnnotations' parameter 'isReactionMol' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCH.h:28: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMolMCH::DrawMolMCH(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCH.h:28: warning: The following parameter of RDKit::MolDraw2D_detail::DrawMolMCH::DrawMolMCH(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) is not documented: parameter 'highlight_radii' Generating docs for compound RDKit::Descriptors::CrippenParams... Generating docs for compound RDKit::Descriptors::Properties... Generating docs for compound RDKit::Descriptors::PropertyFunctor... Generating docs for namespace RDKit::Descriptors::detail Generating docs for namespace RDKit::detail Generating docs for compound RDKit::detail::MCSParametersInternal... Generating docs for namespace RDKit::details Generating docs for namespace RDKit::DGeomHelpers Generating docs for compound RDKit::DGeomHelpers::EmbedParameters... Generating docs for namespace RDKit::DTags Generating docs for namespace RDKit::EnumerationStrategyPickler Generating docs for namespace RDKit::EnumerationTypes Generating docs for namespace RDKit::FileParserUtils Generating docs for namespace RDKit::FilterMatchOps Generating docs for compound RDKit::FilterMatchOps::And... Generating docs for compound RDKit::FilterMatchOps::Not... Generating docs for compound RDKit::FilterMatchOps::Or... Generating docs for namespace RDKit::FMCS Generating docs for compound RDKit::FMCS::Composition2N... Generating docs for compound RDKit::FMCS::DuplicatedSeedCache... Generating docs for nested compound RDKit::FMCS::DuplicatedSeedCache::TKey... Generating docs for compound RDKit::FMCS::ExecStatistics... Generating docs for compound RDKit::FMCS::Graph... Generating docs for compound RDKit::FMCS::MaximumCommonSubgraph... Generating docs for compound RDKit::FMCS::MolFragment... Generating docs for compound RDKit::FMCS::NewBond... Generating docs for compound RDKit::FMCS::Seed... Generating docs for compound RDKit::FMCS::SeedSet... Generating docs for compound RDKit::FMCS::SubstructureCache... Generating docs for nested compound RDKit::FMCS::SubstructureCache::HashKey... Generating docs for nested compound RDKit::FMCS::SubstructureCache::KeyNumericMetrics... Generating docs for compound RDKit::FMCS::Target... Generating docs for compound RDKit::FMCS::TargetMatch... Generating docs for compound RDKit::FMCS::TArray2D... Generating docs for namespace RDKit::ForceFieldsHelper Generating docs for namespace RDKit::ForceFieldsHelper::detail Generating docs for namespace RDKit::GeneralizedSubstruct Generating docs for compound RDKit::GeneralizedSubstruct::ExtendedQueryMol... Generating docs for namespace RDKit::GeneralMolSupplier Generating docs for compound RDKit::GeneralMolSupplier::SupplierOptions... Generating docs for namespace RDKit::GenericGroups Generating docs for namespace RDKit::GenericGroups::Matchers Generating docs for namespace RDKit::Local Generating docs for namespace RDKit::MACCSFingerprints Generating docs for namespace RDKit::MHFPFingerprints Generating docs for compound RDKit::MHFPFingerprints::MHFPEncoder... Generating docs for namespace RDKit::MHFPFingerprints::FNV Generating docs for namespace RDKit::MMFF Generating docs for compound RDKit::MMFF::MMFFAtomProperties... Generating docs for compound RDKit::MMFF::MMFFMolProperties... Generating docs for namespace RDKit::MMFF::DefaultParameters Generating docs for namespace RDKit::MMFF::Tools Generating docs for compound RDKit::MMFF::Tools::DefaultTorsionBondSmarts... Generating docs for namespace RDKit::MMPA Generating docs for namespace RDKit::MolAlign Generating docs for compound RDKit::MolAlign::LAP... Generating docs for compound RDKit::MolAlign::MolAlignException... Generating docs for compound RDKit::MolAlign::MolHistogram... Generating docs for compound RDKit::MolAlign::O3A... Generating docs for compound RDKit::MolAlign::O3AConstraint... Generating docs for compound RDKit::MolAlign::O3AConstraintVect... Generating docs for compound RDKit::MolAlign::O3AFuncData... Generating docs for compound RDKit::MolAlign::SDM... Generating docs for namespace RDKit::MolDraw2D_detail Generating docs for compound RDKit::MolDraw2D_detail::AtomSymbol... Generating docs for compound RDKit::MolDraw2D_detail::DrawAnnotation... Generating docs for compound RDKit::MolDraw2D_detail::DrawMol... Generating docs for compound RDKit::MolDraw2D_detail::DrawMolMCH... Generating docs for compound RDKit::MolDraw2D_detail::DrawMolMCHCi/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h:24: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::DrawMolMCHCircleAndLine(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h:24: warning: The following parameter of RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::DrawMolMCHCircleAndLine(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) is not documented: parameter 'highlight_radii' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h:21: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMolMCHLasso::DrawMolMCHLasso(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h:21: warning: The following parameter of RDKit::MolDraw2D_detail::DrawMolMCHLasso::DrawMolMCHLasso(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) is not documented: parameter 'highlight_radii' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:263: warning: The following parameter of RDKit::MolEnumerator::enumerate(const ROMol &mol, size_t maxPerOperation=0) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/MolInterchange.h:81: warning: The following parameter of RDKit::MolInterchange::MolsToJSONData(const std::vector< T > &mols, const JSONWriteParameters ¶ms=defaultJSONWriteParameters) is not documented: parameter 'params' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/MolInterchange.h:90: warning: The following parameter of RDKit::MolInterchange::MolToJSONData(const T &mol, const JSONWriteParameters ¶ms=defaultJSONWriteParameters) is not documented: parameter 'params' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.h:801: 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-202309.3/Code/GraphMol/MolOps.h:281: warning: The following parameters of RDKit::MolOps::mergeQueryHs(const ROMol &mol, bool mergeUnmappedOnly=false, bool mergeIsotopes=false) are not documented: parameter 'mergeUnmappedOnly' parameter 'mergeIsotopes' rcleAndLine... Generating docs for compound RDKit::MolDraw2D_detail::DrawMolMCHLasso... Generating docs for compound RDKit::MolDraw2D_detail::DrawShape... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeArc... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeArrow... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeDashedWedge... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeEllipse... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapePolyLine... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeSimpleLine... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeSolidWedge... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeWavyLine... Generating docs for compound RDKit::MolDraw2D_detail::DrawText... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextCairo... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFT... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTCairo... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTJS... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTQt... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTSVG... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextJS... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextNotFT... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextQt... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextSVG... Generating docs for compound RDKit::MolDraw2D_detail::StringRect... Generating docs for namespace RDKit::MolDraw2DUtils Generating docs for compound RDKit::MolDraw2DUtils::ContourParams... Generating docs for namespace RDKit::MolEnumerator Generating docs for compound RDKit::MolEnumerator::LinkNode... Generating docs for compound RDKit::MolEnumerator::LinkNodeOp... Generating docs for compound RDKit::MolEnumerator::MolEnumeratorOp... Generating docs for compound RDKit::MolEnumerator::MolEnumeratorParams... Generating docs for compound RDKit::MolEnumerator::PositionVariationOp... Generating docs for compound RDKit::MolEnumerator::RepeatUnitOp... Generating docs for namespace RDKit::MolEnumerator::detail Generating docs for namespace RDKit::MolEnumerator::utils Generating docs for namespace RDKit::MolFragmenter Generating docs for compound RDKit::MolFragmenter::FragmenterBondType... Generating docs for namespace RDKit::MolHash Generating docs for namespace RDKit::MolInterchange Generating docs for compound RDKit::MolInterchange::JSONParseParameters... Generating docs for compound RDKit::MolInterchange::JSONWriteParameters... Generating docs for namespace RDKit::MolOps Generating docs for compound RDKit::MolOps::AdjustQueryParameters... Generating docs for compound RDKit::MolOps::RemoveHsParameters... Generating docs for namespace RDKit::MolOps::details Generating docs for namespace RDKit::MolShapes Generating docs for namespace RDKit::MolStandardize Generating docs for compound RDKit::MolStandardize::AcidBaseCatalogEntry... Generating docs for compound RDKit::MolStandardize::AcidBaseCatalogParams... Generating docs for compound RDKit::MolStandardize::AllowedAtomsValidation... Generating docs for compound RDKit::MolStandardize::ChargeCorrection... Generating docs for compound RDKit::MolStandardize::CleanupParameters... Generating docs for compound RDKit::MolStandardize::DisallowedAtomsValidation... Generating docs for compound RDKit::MolStandardize::FragmentCatalogEntry... Generating docs for compound RDKit::MolStandardize::FragmentCatalogParams... Generating docs for compound RDKit::MolStandardize::FragmentRemover... Generating docs for compound RDKit::MolStandardize::FragmentValidation... Generating docs for compound RDKit::MolStandardize::IsotopeValidation... Generating docs for compound RDKit::MolStandardize::LargestFragmentChooser... Generating docs for nested compound RDKit::MolStandardize::LargestFragmentChooser::Largest... Generating docs for compound RDKit::MolStandardize::MetalDisconnector... Generating docs for compound RDKi/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.h:204: warning: argument 'countSimulation' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.h:204: warning: argument 'includeChirality' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.h:204: warning: argument 'onlyNonzeroInvariants' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.h:262: warning: argument 'countSimulation' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.h:262: warning: argument 'includeChirality' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.h:262: warning: argument 'onlyNonzeroInvariants' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::MorganFingerprint::MorganAtomEnv::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganFingerprints.h:117: 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-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::RDKitFP::RDKitFPAtomEnv::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, bool hashResults=false, const std::uint64_t fpSize=0) const are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.h:26: warning: The following parameter of RDKit::ReducedGraphs::generateMolExtendedReducedGraph(const ROMol &mol, std::vector< boost::dynamic_bitset<> > *atomTypes=nullptr) is not documented: parameter 'atomTypes' t::MolStandardize::MetalDisconnectorOptions... Generating docs for compound RDKit::MolStandardize::MolVSValidation... Generating docs for compound RDKit::MolStandardize::MolVSValidations... Generating docs for compound RDKit::MolStandardize::NeutralValidation... Generating docs for compound RDKit::MolStandardize::NoAtomValidation... Generating docs for compound RDKit::MolStandardize::Normalizer... Generating docs for compound RDKit::MolStandardize::RDKitValidation... Generating docs for compound RDKit::MolStandardize::Reionizer... Generating docs for compound RDKit::MolStandardize::Tautomer... Generating docs for compound RDKit::MolStandardize::TautomerCatalogEntry... Generating docs for compound RDKit::MolStandardize::TautomerCatalogParams... Generating docs for compound RDKit::MolStandardize::TautomerEnumerator... Generating docs for compound RDKit::MolStandardize::TautomerEnumeratorCallback... Generating docs for compound RDKit::MolStandardize::TautomerEnumeratorResult... Generating docs for nested compound RDKit::MolStandardize::TautomerEnumeratorResult::const_iterator... Generating docs for compound RDKit::MolStandardize::TautomerTransform... Generating docs for compound RDKit::MolStandardize::TransformCatalogEntry... Generating docs for compound RDKit::MolStandardize::TransformCatalogParams... Generating docs for compound RDKit::MolStandardize::Uncharger... Generating docs for compound RDKit::MolStandardize::ValidationErrorInfo... Generating docs for compound RDKit::MolStandardize::ValidationMethod... Generating docs for namespace RDKit::MolStandardize::defaults Generating docs for namespace RDKit::MolStandardize::TautomerScoringFunctions Generating docs for namespace RDKit::MorganFingerprint Generating docs for compound RDKit::MorganFingerprint::MorganArguments... Generating docs for compound RDKit::MorganFingerprint::MorganAtomEnv... Generating docs for compound RDKit::MorganFingerprint::MorganAtomInvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganBondInvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganEnvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganFeatureAtomInvGenerator... Generating docs for namespace RDKit::MorganFingerprints Generating docs for compound RDKit::MorganFingerprints::ss_matcher... Generating docs for namespace RDKit::PicklerOps Generating docs for namespace RDKit::PNGData Generating docs for namespace RDKit::QueryOps Generating docs for namespace RDKit::RascalMCES Generating docs for compound RDKit::RascalMCES::PartitionSet... Generating docs for compound RDKit::RascalMCES::RascalClusterOptions... Generating docs for compound RDKit::RascalMCES::RascalOptions... Generating docs for compound RDKit::RascalMCES::RascalResult... Generating docs for namespace RDKit::RascalMCES::details Generating docs for compound RDKit::RascalMCES::details::ClusNode... Generating docs for namespace RDKit::RDKitFP Generating docs for compound RDKit::RDKitFP::RDKitFPArguments... Generating docs for compound RDKit::RDKitFP::RDKitFPAtomEnv... Generating docs for compound RDKit::RDKitFP::RDKitFPAtomInvGenerator... Generating docs for compound RDKit::RDKitFP::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::NetworkEdge... Generating docs for compound RDKit::ScaffoldNetwork::ScaffoldNetwork... Generating docs for compound RDKit::ScaffoldNetwork::ScaffoldNetworkParams... Generating docs for namespace RDKit::ScaffoldNetwork::detail Generating docs for namespace RDKit::SGroupParsing Generating docs for namespace RDKit::SGroupWriting Generating docs for namespace RDKit::SLNParse Generating docs for compound R/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:94: warning: argument 'useCountSimulation' of command @param is not found in the argument list of RDKit::TopologicalTorsion::getTopologicalTorsionGenerator(bool includeChirality=false, uint32_t torsionAtomCount=4, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, bool countSimulation=true, std::uint32_t fpSize=2048, std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, bool ownsAtomInvGen=false) /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:94: warning: The following parameter of RDKit::TopologicalTorsion::getTopologicalTorsionGenerator(bool includeChirality=false, uint32_t torsionAtomCount=4, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, bool countSimulation=true, std::uint32_t fpSize=2048, std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, bool ownsAtomInvGen=false) is not documented: parameter 'countSimulation' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:32: warning: argument 'useCountSimulation' of command @param is not found in the argument list 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) /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:32: 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-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:68: warning: The following parameter of RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::TopologicalTorsionAtomEnv(OutputType bitId, INT_VECT atomPath) is not documented: parameter 'atomPath' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/HierarchicalClusterPicker.h:48: warning: The following parameter of RDPickers::HierarchicalClusterPicker::pick(const double *distMat, unsigned int poolSize, unsigned int pickSize) const is not documented: parameter 'distMat' /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/LeaderPicker.h:48: warning: argument 'firstPicks' of command @param is not found in the argument list of RDPickers::LeaderPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/LeaderPicker.h:48: warning: argument 'seed' of command @param is not found in the argument list of RDPickers::LeaderPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/LeaderPicker.h:87: warning: The following parameters of RDPickers::LeaderPicker::pick(const double *distMat, unsigned int poolSize, unsigned int pickSize, const RDKit::INT_VECT &firstPicks, double threshold, int nthreads) const are not documented: parameter 'threshold' parameter 'nthreads' /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/MaxMinPicker.h:44: warning: argument 'firstPicks' of command @param is not found in the argument list of RDPickers::MaxMinPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/MaxMinPicker.h:44: warning: argument 'seed' of command @param is not found in the argument list of RDPickers::MaxMinPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const DKit::SLNParse::AttribType... Generating docs for namespace RDKit::SmartsWrite Generating docs for namespace RDKit::SmilesWrite Generating docs for namespace RDKit::SmilesWrite::detail Generating docs for namespace RDKit::StructureCheck Generating docs for compound RDKit::StructureCheck::AugmentedAtom... Generating docs for compound RDKit::StructureCheck::ChargeFix... Generating docs for compound RDKit::StructureCheck::IncEntry... Generating docs for compound RDKit::StructureCheck::Ligand... Generating docs for compound RDKit::StructureCheck::Neighbourhood... Generating docs for compound RDKit::StructureCheck::PathEntry... Generating docs for compound RDKit::StructureCheck::StructChecker... Generating docs for compound RDKit::StructureCheck::StructCheckerOptions... Generating docs for compound RDKit::StructureCheck::StructCheckTautomer... Generating docs for namespace RDKit::Subgraphs Generating docs for namespace RDKit::SubstanceGroupChecks Generating docs for namespace RDKit::TopologicalTorsion Generating docs for compound RDKit::TopologicalTorsion::TopologicalTorsionArguments... Generating docs for compound RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv... Generating docs for compound RDKit::TopologicalTorsion::TopologicalTorsionEnvGenerator... Generating docs for namespace RDKit::UFF Generating docs for namespace RDKit::UFF::Tools Generating docs for compound RDKit::UFF::Tools::DefaultTorsionBondSmarts... Generating docs for namespace RDKit::Utils Generating docs for compound RDKit::Utils::LocaleSwitcher... Generating docs for namespace RDKit::Utils::detail Generating docs for namespace RDLog Generating docs for namespace RDNumeric Generating docs for compound RDNumeric::Matrix... Generating docs for compound RDNumeric::SquareMatrix... Generating docs for compound RDNumeric::SymmMatrix... Generating docs for compound RDNumeric::Vector... Generating docs for namespace RDNumeric::Alignments Generating docs for namespace RDNumeric::EigenSolvers Generating docs for namespace RDPickers Generating docs for compound RDPickers::DistPicker... Generating docs for compound RDPickers::HierarchicalClusterPicker... Generating docs for compound RDPickers::LeaderPicker... Generating docs for compound RDPickers::LeaderPickerState... Generating docs for compound RDPickers::MaxMinPicker... Generating docs for compound RDPickers::MaxMinPickInfo... Generating docs for namespace RingUtils Generating docs for namespace SmilesParseOps Generating docs for namespace SmilesParseOps::detail Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating topic index... Generating module index... Generating module member index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... type lookup cache used 33473/65536 hits=200049 misses=37089 symbol lookup cache used 29447/65536 hits=269120 misses=29447 finished... (cd /build/reproducible-path/rdkit-202309.3/Docs/Book; RDBASE=/build/reproducible-path/rdkit-202309.3 /usr/bin/make html) make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/Docs/Book' mkdir -p _build/html/cppapi cp -r /build/reproducible-path/rdkit-202309.3/Code/docs/* _build/html/cppapi cp -r C++Examples _build/html/ sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v7.2.6 WARNING: html_static_path entry '_static' does not exist myst v3.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=set(), disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 308 source files that are out of date updating environment: [new config] 308 added, 0 changed, 0 removed reading sources... 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[ 87%] source/rdkit.ML.Neural.Network reading sources... [ 87%] source/rdkit.ML.Neural.Trainers reading sources... [ 88%] source/rdkit.ML.SLT reading sources... [ 88%] source/rdkit.ML.SLT.Risk reading sources... [ 88%] source/rdkit.ML.Scoring reading sources... [ 89%] source/rdkit.ML.Scoring.Scoring reading sources... [ 89%] source/rdkit.ML.ScreenComposite reading sources... [ 89%] source/rdkit.ML.files reading sources... [ 90%] source/rdkit.Numerics reading sources... [ 90%] source/rdkit.Numerics.rdAlignment reading sources... [ 90%] source/rdkit.RDConfig reading sources... [ 91%] source/rdkit.RDLogger reading sources... [ 91%] source/rdkit.RDPaths reading sources... [ 91%] source/rdkit.RDRandom reading sources... [ 92%] source/rdkit.SimDivFilters reading sources... [ 92%] source/rdkit.SimDivFilters.SimilarityPickers reading sources... [ 92%] source/rdkit.SimDivFilters.rdSimDivPickers reading sources... [ 93%] source/rdkit.TestRunner reading sources... [ 93%] source/rdkit.VLib reading sources... [ 93%] source/rdkit.VLib.Filter reading sources... [ 94%] source/rdkit.VLib.Node reading sources... [ 94%] source/rdkit.VLib.NodeLib reading sources... [ 94%] source/rdkit.VLib.NodeLib.DbMolSupply reading sources... [ 94%] source/rdkit.VLib.NodeLib.DbPickleSupplier reading sources... [ 95%] source/rdkit.VLib.NodeLib.SDSupply reading sources... [ 95%] source/rdkit.VLib.NodeLib.SmartsMolFilter reading sources... [ 95%] source/rdkit.VLib.NodeLib.SmartsRemover reading sources... [ 96%] source/rdkit.VLib.NodeLib.SmilesDupeFilter reading sources... [ 96%] source/rdkit.VLib.NodeLib.SmilesOutput reading sources... [ 96%] source/rdkit.VLib.NodeLib.SmilesSupply reading sources... [ 97%] source/rdkit.VLib.Output reading sources... [ 97%] source/rdkit.VLib.Supply reading sources... [ 97%] source/rdkit.VLib.Transform reading sources... [ 98%] source/rdkit.rdBase reading sources... [ 98%] source/rdkit.six reading sources... [ 98%] source/rdkit.utils reading sources... [ 99%] source/rdkit.utils.cactvs reading sources... [ 99%] source/rdkit.utils.chemutils reading sources... [ 99%] source/rdkit.utils.fileutils reading sources... [100%] source/rdkit.utils.listutils reading sources... [100%] source/rdkit.utils.spiral /build/reproducible-path/rdkit-202309.3/Docs/Book/BackwardsIncompatibleChanges.md:49: WARNING: duplicate label changes to canonicalization, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/BackwardsIncompatibleChanges.md /build/reproducible-path/rdkit-202309.3/Docs/Book/Cartridge.md:732: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/BackwardsIncompatibleChanges.md /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst:1733: WARNING: Title underline too short. Contiguous Rotatable Bonds ========================= /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst:1733: WARNING: Title underline too short. Contiguous Rotatable Bonds ========================= /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst:7: WARNING: duplicate label introduction, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Cartridge.md /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst:10: WARNING: duplicate label what is this?, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Cartridge.md /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst:2501: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Cartridge.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md:3: WARNING: duplicate label what is this?, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md:305: WARNING: duplicate label writing molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:358: WARNING: Explicit markup ends without a blank line; unexpected unindent. /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:12: WARNING: duplicate label what is this?, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:30: WARNING: duplicate label reading single molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:104: WARNING: duplicate label reading sets of molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:208: WARNING: duplicate label writing molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:390: WARNING: duplicate label writing sets of molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:431: WARNING: duplicate label working with molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:435: WARNING: duplicate label looping over atoms and bonds, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:478: WARNING: duplicate label ring information, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:547: WARNING: duplicate label modifying molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:615: WARNING: duplicate label working with 2d molecules: generating depictions, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:665: WARNING: duplicate label working with 3d molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:788: WARNING: duplicate label preserving molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:844: WARNING: duplicate label drawing molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:1083: WARNING: duplicate label substructure searching, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:1148: WARNING: duplicate label stereochemistry in substructure matches, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:1186: WARNING: duplicate label atom map indices in smarts, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:3425: WARNING: duplicate label the sssr problem, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:3829: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/Install.md:226: WARNING: Non-consecutive header level increase; H4 to H6 [myst.header] /build/reproducible-path/rdkit-202309.3/Docs/Book/Install.md:450: WARNING: duplicate label recommended extras, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Install.md /build/reproducible-path/rdkit-202309.3/Docs/Book/Install.md:494: WARNING: duplicate label testing the build (optional, but recommended), other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Install.md /build/reproducible-path/rdkit-202309.3/Docs/Book/Install.md:499: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/Overview.md:145: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Install.md /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:1563: ERROR: Malformed table. Text in column margin in table line 15. ======================== ========= Alkyl (ALK) alkyl side chains (not an H atom) AlkylH (ALH) alkyl side chains including an H atom Alkenyl (AEL) alkenyl side chains AlkenylH (AEH) alkenyl side chains or an H atom Alkynyl (AYL) alkynyl side chains AlkynylH (AYH) alkynyl side chains or an H atom Alkoxy (AOX) alkoxy side chains AlkoxyH (AOH) alkoxy side chains or an H atom Carbocyclic (CBC) carbocyclic side chains CarbocyclicH (CBH) carbocyclic side chains or an H atom Carbocycloalkyl (CAL) cycloalkyl side chains CarbocycloalkylH (CAH) cycloalkyl side chains or an H atom Carbocycloalkenyl (CEL) cycloalkenyl side chains CarbocycloalkenylH (CEH) cycloalkenyl side chains or an H atom Carboaryl (ARY) all-carbon aryl side chains CarboarylH (ARH) all-carbon aryl side chains or an H atom Cyclic (CYC) cyclic side chains CyclicH (CYH) cyclic side chains or an H atom Acyclic(ACY) acyclic side chains (not an H atom) AcyclicH (ACH) acyclic side chains or an H atom Carboacyclic (ABC) all-carbon acyclic side chains CarboacyclicH (ABH) all-carbon acyclic side chains or an H atom Heteroacyclic (AHC) acyclic side chains with at least one heteroatom HeteroacyclicH (AHH) acyclic side chains with at least one heteroatom or an H atom Heterocyclic (CHC) cyclic side chains with at least one heteroatom HeterocyclicH (CHH) cyclic side chains with at least one heteroatom or an H atom Heteroaryl (HAR) aryl side chains with at least one heteroatom HeteroarylH (HAH) aryl side chains with at least one heteroatom or an H atom NoCarbonRing (CXX) ring containing no carbon atoms NoCarbonRingH (CXH) ring containing no carbon atoms or an H atom Group (G) any group (not H atom) GroupH (GH) any group (including H atom) Group* (G*) any group with a ring closure GroupH* (GH*) any group with a ring closure or an H atom ======================== ========= /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:1664: WARNING: Enumerated list ends without a blank line; unexpected unindent. /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:180: WARNING: duplicate label aromaticity, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:385: WARNING: duplicate label dative bonds, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:536: WARNING: duplicate label stereochemistry, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:1264: WARNING: duplicate label chemical features, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:2200: WARNING: duplicate label introduction, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:2298: WARNING: duplicate label rdkit fingerprints, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:2464: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Overview.md WARNING: autodoc: failed to import module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Avalon' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Avalon.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Avalon.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.rst WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rst:28: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Avalon.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rst:113: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Avalon.rst WARNING: autodoc: failed to import module 'Chem.AllChem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.AtomPairs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.AtomPairs.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rst WARNING: autodoc: failed to import module 'Chem.AtomPairs.Pairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Sheridan' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Torsions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.BRICS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.BuildFragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.ChemUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.AtomPairs.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.ChemUtils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.AtomPairs.rst WARNING: autodoc: failed to import module 'Chem.ChemUtils.AlignDepict' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.BulkTester' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.DescriptorUtilities' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.SDFToCSV' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.TemplateExpand' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemicalForceFields' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Crippen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Descriptors3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Draw.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.ChemUtils.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Draw.rst:21: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.ChemUtils.rst WARNING: autodoc: failed to import module 'Chem.Draw.IPythonConsole' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.MolDrawing' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.SimilarityMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.aggCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.cairoCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.canvasbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.mplCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.qtCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2DQt' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.EState.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Draw.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.EState.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Draw.rst WARNING: autodoc: failed to import module 'Chem.EState.AtomTypes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.EState_VSA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.Fingerprinter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EnumerateHeterocycles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EnumerateStereoisomers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FastSDMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatFinderCLI' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.FeatMaps.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.EState.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.FeatMaps.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.EState.rst WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapParser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapPoint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Features.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.FeatMaps.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Features.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.FeatMaps.rst WARNING: autodoc: failed to import module 'Chem.Features.FeatDirUtilsRD' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features.ShowFeats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FilterCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Fingerprints.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Features.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Fingerprints.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Features.rst WARNING: autodoc: failed to import module 'Chem.Fingerprints.ClusterMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.DbFpSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.FingerprintMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.MolSimilarity' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.SimilarityScreener' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fraggle' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Fraggle.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Fingerprints.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Fraggle.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Fingerprints.rst WARNING: autodoc: failed to import module 'Chem.Fraggle.FraggleSim' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FragmentMatcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fragments' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FunctionalGroups' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.GraphDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Graphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Lipinski' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MACCSkeys' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolDb.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Fraggle.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolDb.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Fraggle.rst WARNING: autodoc: failed to import module 'Chem.MolDb.FingerprintUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_orig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_sa' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolKey.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolDb.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolKey.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolDb.rst WARNING: autodoc: failed to import module 'Chem.MolKey.InchiInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolStandardize.rst:6: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolKey.rst WARNING: autodoc: failed to import module 'Chem.MolStandardize.rdMolStandardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolSurf' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PandasTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PeriodicTable' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Pharm2D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolStandardize.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Pharm2D.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolKey.rst WARNING: autodoc: failed to import module 'Chem.Pharm2D.Generate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Gobbi_Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Matcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.SigFactory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Pharm3D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Pharm2D.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Pharm3D.rst:14: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Pharm2D.rst WARNING: autodoc: failed to import module 'Chem.Pharm3D.EmbedLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.ExcludedVolume' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.Pharmacophore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PropertyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.QED' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Randomize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Recap' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.RegistrationHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SATIS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SaltRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Scaffolds.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Pharm3D.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Scaffolds.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Pharm3D.rst WARNING: autodoc: failed to import module 'Chem.Scaffolds.MurckoScaffold' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds.rdScaffoldNetwork' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ShowMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SimpleEnum' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Scaffolds.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Scaffolds.rst WARNING: autodoc: failed to import module 'Chem.SimpleEnum.Enumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SpacialScore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Subshape.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.SimpleEnum.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Subshape.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.SimpleEnum.rst WARNING: autodoc: failed to import module 'Chem.Subshape.BuilderUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeAligner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeBuilder' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeObjects' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Suppliers.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Subshape.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Suppliers.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Subshape.rst WARNING: autodoc: failed to import module 'Chem.Suppliers.DbMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers.MolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.TemplateAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.TorsionFingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.fmcs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Suppliers.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.fmcs.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Suppliers.rst WARNING: autodoc: failed to import module 'Chem.fmcs.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.inchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdAbbreviations' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdCIPLabeler' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdChemReactions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rdChemicalFeatures.rst:2: WARNING: Title underline too short. rdkit.Chem.rdChemicalFeatures module ================================= WARNING: autodoc: failed to import module 'Chem.rdChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdCoordGen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDepictor' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDeprotect' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDetermineBonds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdEHTTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFMCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFingerprintGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rdForceFieldHelpers.rst:2: WARNING: Title underline too short. rdkit.Chem.rdForceFieldHelpers module ================================= WARNING: autodoc: failed to import module 'Chem.rdForceFieldHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFreeSASA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMHFPFingerprint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMMPA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rdMolChemicalFeatures.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolChemicalFeatures module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rdMolDescriptors.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolDescriptors module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolEnumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rdMolInterchange.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolInterchange module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolInterchange' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolTransforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rdPartialCharges.rst:2: WARNING: Title underline too short. rdkit.Chem.rdPartialCharges module ================================= WARNING: autodoc: failed to import module 'Chem.rdPartialCharges' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rdRGroupDecomposition.rst:2: WARNING: Title underline too short. rdkit.Chem.rdRGroupDecomposition module ================================= WARNING: autodoc: failed to import module 'Chem.rdRGroupDecomposition' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdSLNParse' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdShapeHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rdSubstructLibrary.rst:2: WARNING: Title underline too short. rdkit.Chem.rdSubstructLibrary module ================================= WARNING: autodoc: failed to import module 'Chem.rdSubstructLibrary' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdTautomerQuery' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdchem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdfiltercatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdfragcatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdinchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdmolfiles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdmolops' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdqueries' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdtrajectory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataManip' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataManip.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataManip.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.fmcs.rst WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataManip.Metric.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.fmcs.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataManip.Metric.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataManip.rst WARNING: autodoc: failed to import module 'DataManip.Metric.rdMetricMatrixCalc' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataStructs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataManip.Metric.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataStructs.rst:18: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataManip.Metric.rst WARNING: autodoc: failed to import module 'DataStructs.BitEnsemble' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitEnsembleDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.LazySignature' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.TopNContainer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.VectCollection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.cDataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Dbase.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataStructs.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Dbase.rst:18: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataStructs.rst WARNING: autodoc: failed to import module 'Dbase.DbConnection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbModule' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbReport' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbResultSet' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.StorageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DistanceGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DistanceGeometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Dbase.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DistanceGeometry.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Dbase.rst WARNING: autodoc: failed to import module 'DistanceGeometry.DistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ForceField.rst:5: WARNING: Block quote ends without a blank line; unexpected unindent. WARNING: autodoc: failed to import module 'ForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ForceField.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DistanceGeometry.rst WARNING: autodoc: failed to import module 'ForceField.rdForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Geometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Geometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DistanceGeometry.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Geometry.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ForceField.rst WARNING: autodoc: failed to import module 'Geometry.rdGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataManip.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.rst:24: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Geometry.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.rst:38: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Geometry.rst WARNING: autodoc: failed to import module 'ML.AnalyzeComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.BuildComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Cluster.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Cluster.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.rst WARNING: autodoc: failed to import module 'ML.Cluster.Butina' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.ClusterUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.ClusterVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Clustering' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Clusters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Murtagh' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Resemblance' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Standardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Composite.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Cluster.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Composite.rst:14: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Cluster.rst WARNING: autodoc: failed to import module 'ML.Composite.AdjustComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.BayesComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.Composite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.CompositeRun' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Data.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Composite.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Data.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Composite.rst WARNING: autodoc: failed to import module 'ML.Data.DataUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.FindQuantBounds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.MLData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Quantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.SplitData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Stats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Transforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.cQuantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.DecTree.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Data.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.DecTree.rst:23: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Data.rst WARNING: autodoc: failed to import module 'ML.DecTree.BuildQuantTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.BuildSigTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.Forest' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.ID3' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.PruneTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.QuantTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.SigTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.Tree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.TreeUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.TreeVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Descriptors.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.DecTree.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Descriptors.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.DecTree.rst WARNING: autodoc: failed to import module 'ML.Descriptors.CompoundDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.MoleculeDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.Parser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.EnrichPlot' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.GrowComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.InfoTheory.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Descriptors.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.InfoTheory.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Descriptors.rst WARNING: autodoc: failed to import module 'ML.InfoTheory.BitClusterer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.BitRank' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.entropy' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.InfoTheory.rdInfoTheory.rst:2: WARNING: Title underline too short. rdkit.ML.InfoTheory.rdInfoTheory module ====================================== WARNING: autodoc: failed to import module 'ML.InfoTheory.rdInfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.KNN.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.InfoTheory.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.KNN.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.InfoTheory.rst WARNING: autodoc: failed to import module 'ML.KNN.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.DistFunctions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNClassificationModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNRegressionModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MLUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.MLUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.KNN.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.MLUtils.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.KNN.rst WARNING: autodoc: failed to import module 'ML.MLUtils.VoteImg' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MatOps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.ModelPackage.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.MLUtils.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.ModelPackage.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.MLUtils.rst WARNING: autodoc: failed to import module 'ML.ModelPackage.PackageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage.Packager' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.NaiveBayes.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.ModelPackage.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.NaiveBayes.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.ModelPackage.rst WARNING: autodoc: failed to import module 'ML.NaiveBayes.ClassificationModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Neural.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.NaiveBayes.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Neural.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.NaiveBayes.rst WARNING: autodoc: failed to import module 'ML.Neural.ActFuncs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.NetNode' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.Network' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.Trainers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.SLT' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.SLT.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Neural.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.SLT.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Neural.rst WARNING: autodoc: failed to import module 'ML.SLT.Risk' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Scoring.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.SLT.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Scoring.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.SLT.rst WARNING: autodoc: failed to import module 'ML.Scoring.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ScreenComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.files' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Numerics' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Numerics.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Scoring.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Numerics.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Scoring.rst WARNING: autodoc: failed to import module 'Numerics.rdAlignment' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDConfig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDLogger' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDPaths' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDRandom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.SimDivFilters.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Numerics.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.SimDivFilters.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Numerics.rst WARNING: autodoc: failed to import module 'SimDivFilters.SimilarityPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters.rdSimDivPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'TestRunner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.rst:12: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.SimDivFilters.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.rst:23: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.SimDivFilters.rst WARNING: autodoc: failed to import module 'VLib.Filter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Node' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.NodeLib.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.NodeLib.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.rst WARNING: autodoc: failed to import module 'VLib.NodeLib.DbMolSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.DbPickleSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SDSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsMolFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesDupeFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesOutput' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Output' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Supply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Transform' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'rdBase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'six' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.utils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.NodeLib.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.utils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.NodeLib.rst WARNING: autodoc: failed to import module 'utils.cactvs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.fileutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.listutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.spiral' from module 'rdkit'; the following exception was raised: No module named 'rdkit' looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/rdkit-202309.3/Docs/Book/data/README.md: WARNING: document isn't included in any toctree /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.SpacialScore.rst: WARNING: document isn't included in any toctree done preparing documents... done copying assets... copying downloadable files... 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[100%] images/query_atoms.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 444 warnings. The HTML pages are in _build/html. Build finished. The HTML pages are in _build/html. make[2]: Leaving directory '/build/reproducible-path/rdkit-202309.3/Docs/Book' # (cd /build/reproducible-path/rdkit-202309.3/Docs/Book; RDBASE=/build/reproducible-path/rdkit-202309.3 /usr/bin/make latexpdf) make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' cp -r rdkit obj-*/ find /build/reproducible-path/rdkit-202309.3 -name rdchem.so /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit/Chem/rdchem.so #export RDBASE=/build/reproducible-path/rdkit-202309.3 PYTHONPATH=/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu//lib:/usr/lib/libeatmydata" PYTHONPATH=/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/:/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu//lib:/usr/lib/libeatmydata" dh_auto_test cd obj-i686-linux-gnu && make -j11 test ARGS\+=--verbose ARGS\+=-j11 make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j11 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/DartConfiguration.tcl Add coverage exclude regular expressions. UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: testCoordGen 1: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/CoordGen/testCoordGen 1: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/CoordGen 1: Test timeout computed to be: 1500 test 2 Start 2: pyCoordGen 2: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/External/CoordGen/Wrap/testCoordGen.py" 2: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/CoordGen/Wrap 2: Test timeout computed to be: 1500 test 3 Start 3: testDict 3: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral/testDict 3: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral 3: Test timeout computed to be: 1500 test 4 Start 4: testRDValue 4: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral/testRDValue 4: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral 4: Test timeout computed to be: 1500 test 5 Start 5: testConcurrentQueue 5: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral/testConcurrentQueue 5: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral 5: Test timeout computed to be: 1500 test 6 Start 6: dictTestsCatch 6: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral/dictTestsCatch 6: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral 6: Test timeout computed to be: 1500 test 7 Start 7: logTestsCatch 7: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral/logTestsCatch 7: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral 7: Test timeout computed to be: 1500 test 8 Start 8: testDataStructs 8: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/testDataStructs 8: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs 8: Test timeout computed to be: 1500 test 9 Start 9: testFPB 9: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/testFPB 9: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs 9: Test timeout computed to be: 1500 test 10 Start 10: testMultiFPB 10: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/testMultiFPB 10: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs 10: Test timeout computed to be: 1500 test 11 Start 11: pyBV 11: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/testBV.py" 11: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/Wrap 11: Test timeout computed to be: 1500 3: [21:31:29] Testing Github940: property dictionaries leaking memory 3: [21:31:29] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect 4: -- running tests -- 4: min: -2147483648 -2147483648 4: min: 0 0 4: min: 2.22507e-308 2.22507e-308 4: min: 1.17549e-38 1.17549e-38 4: min: 0 0 4: == int 4: == double 4: == float 4: == unsigned int 4: == bool 4: == std::string 5: [21:31:29] 5: ----------------------------------------- 5: [21:31:29] Finished: testPushAndPop() 5: [21:31:29] 5: ----------------------------------------- 5: [21:31:29] 5: ----------------------------------------- 6: Randomness seeded to: 4095236742 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: 8: 10, 11, 14, 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, 8: t1&t2: 10, 11, 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except 8: 10, 11, 14, 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, 8: t1&t2: 10, 11, 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except 1/222 Test #4: testRDValue ............................ Passed 0.05 sec 2/222 Test #6: dictTestsCatch ......................... Passed 0.04 sec 3/222 Test #8: testDataStructs ........................ Passed 0.02 sec test 12 Start 12: pyDiscreteValueVect 12: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/testDiscreteValueVect.py" 12: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/Wrap 12: Test timeout computed to be: 1500 test 13 Start 13: pySparseIntVect 13: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/testSparseIntVect.py" 13: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/Wrap 13: Test timeout computed to be: 1500 test 14 Start 14: pyFPB 14: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/testFPB.py" 14: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/Wrap 14: Test timeout computed to be: 1500 7: [21:31:29] should not be silent 7: [21:31:29] should not be silent 7: Randomness seeded to: 2828129829 7: [21:31:29] should not be silent 7: [21:31:29] should not be silent 7: [21:31:29] should not be silent 7: [21:31:29] should not be silent 7: [21:31:29] should not be silent 7: [21:31:29] should not be silent 7: [21:31:29] should not be silent 7: [21:31:29] should not be silent 7: =============================================================================== 7: All tests passed (26 assertions in 3 test cases) 7: 4/222 Test #7: logTestsCatch .......................... Passed 0.05 sec test 15 Start 15: testTransforms 15: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/testTransforms 15: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry 15: Test timeout computed to be: 1500 5/222 Test #9: testFPB ................................ Passed 0.04 sec test 16 Start 16: testGrid 16: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/testGrid 16: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry 16: Test timeout computed to be: 1500 15: **************************************** 15: testPointND 15: **************************************** 15: testPointOps3D 15: **************************************** 15: testPointOps2D 15: **************************************** 15: test12D 15: ref1: 0.977421 4.566 ref2: 0.55703 0.297884 15: pt1: 3.22725 1.44987 pt2: 4.8063 1.52008 15: **************************************** 15: test23D 15: **************************************** 15: test3MatMultiply 15: Pt1: 1 0 0 Pt2: 2 0 0 15: -Pt1: -1 -0 -0 15: tp1: 0 0 0 tp2: 0 0 0 15: tp1: 0 0 0 tp2: 0 0 0 15: tp1: 0 0 3 tp2: 0 0 3 15: npt1: 0 0 3 npt2: 0 0 4 15: Pt1: 0 0 3 Pt2: 6.12323e-17 0 4 15: **************************************** 15: testFromQuaternion 15: **************************************** 6/222 Test #15: testTransforms ......................... Passed 0.01 sec test 17 Start 17: geometryTestsCatch 17: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/geometryTestsCatch 17: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry 17: Test timeout computed to be: 1500 17: Randomness seeded to: 2486307435 17: =============================================================================== 17: All tests passed (50 assertions in 5 test cases) 17: 7/222 Test #17: geometryTestsCatch ..................... Passed 0.02 sec test 18 Start 18: testPyGeometry 18: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/testGeometry.py" 18: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/Wrap 18: Test timeout computed to be: 1500 16: *********************************************************** 16: Testing Grid 16: --------------------------------- 16: testUniformGrid1 16: 16: --------------------------------- 16: testUniformGrid2 16: 16: --------------------------------- 16: testUniformGridPickling 16: 16: --------------------------------- 16: testGridOps 16: 16: --------------------------------- 16: testUniformGridIndexing 16: 8/222 Test #16: testGrid ............................... Passed 0.05 sec test 19 Start 19: testMatrices 19: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/testMatrices 19: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics 19: Test timeout computed to be: 1500 9/222 Test #10: testMultiFPB ........................... Passed 0.09 sec test 20 Start 20: testConrec 20: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/testConrec 20: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics 20: Test timeout computed to be: 1500 19: [21:31:29] ----------------------------------------- 19: [21:31:29] Testing RDNumerics: vectors and matrices Code 19: [21:31:29] --------------------------------------- 19: [21:31:29] test1Vector 19: [21:31:29] --------------------------------------- 19: [21:31:29] test2Matrix 19: [21:31:29] --------------------------------------- 19: [21:31:29] test3SquareMatrix 19: [21:31:29] --------------------------------------- 19: [21:31:29] test4SymmMatrix 10/222 Test #19: testMatrices ........................... Passed 0.01 sec test 21 Start 21: testAlignment 21: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment/testAlignment 21: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment 21: Test timeout computed to be: 1500 21: ----------------------------------------- 21: Testing Alignment Code 21: --------------------------------------- 21: testBasic 21: --------------------------------------- 21: testTriangle 21: --------------------------------------- 21: testFourPts 21: --------------------------------------- 21: testReflection 21: --------------------------------------- 11/222 Test #21: testAlignment .......................... Passed 0.03 sec test 22 Start 22: pyAlignment 22: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/Wrap/testAlignment.py" 22: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap 22: Test timeout computed to be: 1500 20: Randomness seeded to: 2277883410 20: 20: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 20: testConrec is a Catch2 v3.4.0 host application. 20: Run with -? for options 20: 20: ------------------------------------------------------------------------------- 20: connectLineSegments 20: basics 20: ------------------------------------------------------------------------------- 20: ./Code/Numerics/testConrec.cpp:90 20: ............................................................................... 20: 20: ./Code/Numerics/testConrec.cpp:130: FAILED: 20: CHECK( contours.size() == 74 ) 20: with expansion: 20: 183 == 74 20: 20: =============================================================================== 20: test cases: 3 | 2 passed | 1 failed 20: assertions: 185 | 184 passed | 1 failed 20: 1: core 1: RDKit 2D 1: 1: 4 4 0 0 0 0 0 0 0 0999 V2000 1: 0.6824 0.1850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.1850 -0.6824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.6824 -0.1850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1850 0.6824 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 1 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 7 7 0 0 0 0 0 0 0 0999 V2000 1: 0.6496 0.9080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3926 -0.0584 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4726 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3396 -0.0616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2048 -0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.3590 -0.3156 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.6160 0.6508 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 1 1 0 1: M END 1: 12/222 Test #20: testConrec .............................***Failed 0.05 sec Randomness seeded to: 2277883410 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ testConrec is a Catch2 v3.4.0 host application. Run with -? for options ------------------------------------------------------------------------------- connectLineSegments basics ------------------------------------------------------------------------------- ./Code/Numerics/testConrec.cpp:90 ............................................................................... ./Code/Numerics/testConrec.cpp:130: FAILED: CHECK( contours.size() == 74 ) with expansion: 183 == 74 =============================================================================== test cases: 3 | 2 passed | 1 failed assertions: 185 | 184 passed | 1 failed test 23 Start 23: testOptimizer 23: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer/testOptimizer 23: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer 23: Test timeout computed to be: 1500 1: templated 1: RDKit 2D 1: 1: 7 7 0 0 0 0 0 0 0 0999 V2000 1: 0.6824 0.1850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.1850 -0.6824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.6824 -0.1850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1850 0.6824 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 1 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 10 10 0 0 0 0 0 0 0 0999 V2000 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 1 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 12 12 0 0 0 0 0 0 0 0999 V2000 1: 0.2846 -0.7516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2790 -1.7516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5898 -2.2466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4530 -1.7418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4476 -0.7418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5788 -0.2468 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5732 0.7532 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2956 1.2484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3012 2.2482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.1700 2.7434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.1590 0.7434 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.1534 -0.2564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 8 11 1 0 1: 11 12 1 0 1: 12 1 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 12 12 0 0 0 0 0 0 0 0999 V2000 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 8 11 1 0 1: 11 12 1 0 1: 12 1 1 0 1: M END 1: 23: ------------------------------------- 23: Testing linear search. 23: done 23: ------------------------------------- 23: Testing BFGS optimization. 23: done 1: core 1: RDKit 2D 1: 1: 10 10 0 0 0 0 0 0 0 0999 V2000 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 1 1 0 1: M END 1: 13/222 Test #23: testOptimizer .......................... Passed 0.01 sec test 24 Start 24: testUFFForceField 24: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/UFF/testUFFForceField 24: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/UFF 24: Test timeout computed to be: 1500 1: core+sidechain 1: RDKit 2D 1: 1: 16 16 0 0 0 0 0 0 0 0999 V2000 1: 1.7868 0.7799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.6532 1.2791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.5187 0.7785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.5180 -0.2215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.6515 -0.7209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7860 -0.2201 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.9195 -0.7195 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0539 -0.2189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8124 -0.7181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.6780 -0.2175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.5445 -0.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.4101 -0.2161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.2764 -0.7153 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.1421 -0.2147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0547 0.7811 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.9211 1.2805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 11 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 8 15 1 0 1: 15 16 1 0 1: 16 1 1 0 1: M END 1: 3: static boost any:0.188861 s 1: templated 1: RDKit 2D 1: 1: 16 16 0 0 0 0 0 0 0 0999 V2000 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 11 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 8 15 1 0 1: 15 16 1 0 1: 16 1 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 9 10 0 0 0 0 0 0 0 0999 V2000 1: 0.6718 -0.9994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5374 -0.4988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5366 0.5012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6702 1.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1954 0.4998 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1946 -0.5002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1454 -0.8098 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.7338 -0.0014 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1466 0.8082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 6 1 1 0 1: 9 5 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 19 21 0 0 0 0 0 0 0 0999 V2000 1: -0.5657 -0.9286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4321 -0.4294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2977 -0.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2969 -1.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.1625 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4329 0.5708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5673 1.0714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5681 2.0714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2975 2.5720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2975 2.5728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.7969 3.4386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2991 0.5720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2999 -0.4278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2513 -0.7362 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5609 -1.6870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5393 -1.8942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8923 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.8381 0.0734 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2499 0.8820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 7 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 14 15 1 0 1: 15 16 1 0 1: 15 17 1 0 1: 14 18 1 0 1: 18 19 1 0 1: 13 1 1 0 1: 19 12 1 0 1: 11 9 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 19 21 0 0 0 0 0 0 0 0999 V2000 1: 0.5360 -0.9365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4021 -0.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2680 -0.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2680 -1.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4020 -2.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4021 0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5360 1.0633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5360 2.0634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.3300 2.5633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3300 2.5633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8300 3.4295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.3300 0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.3300 -0.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2812 -0.7457 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.5900 -1.6966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.9208 -2.4398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.5682 -1.9046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.8686 0.0634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2812 0.8725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 7 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 14 15 1 0 1: 15 16 1 0 1: 15 17 1 0 1: 14 18 1 0 1: 18 19 1 0 1: 13 1 1 0 1: 19 12 1 0 1: 11 9 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 5 4 0 0 0 0 0 0 0 0999 V2000 1: 1.2134 -0.4976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3464 0.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3444 1.0006 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5186 -0.5010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3856 -0.0028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 1 0 1: 4 5 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 7 6 0 0 0 0 0 0 0 0999 V2000 1: -1.7333 -0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8661 -0.0697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8641 0.9303 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0011 -0.5713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8659 -0.0731 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8679 0.9269 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7309 -0.5749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 5 7 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 7 6 0 0 0 0 0 0 0 0999 V2000 1: 1.2184 -0.5011 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3464 0.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3450 1.0068 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5242 -0.5035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3910 -0.0046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2564 -0.5056 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3922 0.9954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 5 7 1 0 1: M END 1: 1: test1 1: RDKit 2D 1: 1: 12 12 0 0 0 0 0 0 0 0999 V2000 1: 0.3628 0.5403 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5014 1.0435 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3692 0.5467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2334 1.0497 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.1012 0.5529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3728 -0.4533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5086 -0.9565 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3594 -0.4597 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2234 -0.9627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.0912 -0.4657 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.0948 0.5341 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.9554 -0.9689 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 2 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 3 6 2 0 1: 6 7 1 0 1: 7 8 2 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 2 0 1: 10 12 1 0 1: 8 1 1 0 1: M END 1: 1: test2 1: RDKit 2D 1: 1: 5 4 0 0 0 0 0 0 0 0999 V2000 1: -0.4980 0.7210 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0004 -0.1464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8678 -0.6440 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5020 0.7182 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8642 -0.6488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 1 0 1: 2 5 1 0 1: M END 1: 24: ------------------------------------- 24: Unit tests for force field basics. 24: done 24: ------------------------------------- 24: Unit tests for basics of UFF bond-stretch terms. 24: done 24: ------------------------------------- 24: Unit tests for UFF bond-stretch terms. 24: done 24: ------------------------------------- 24: Unit tests for basics of UFF angle terms. 24: done 24: ------------------------------------- 24: Unit tests for UFF angle-bend terms. 24: theta = 3.14159; theta0 = 3.14159 24: theta = 2.094395, param1.theta0 = 2.094395 24: done 24: ------------------------------------- 24: Test Simple UFF molecule optimizations. 24: done 24: ------------------------------------- 24: Unit tests for UFF nonbonded terms. 24: done 24: ------------------------------------- 24: Test UFF torsional terms. 24: done 24: ------------------------------------- 24: Test UFF Parameter objects 24: ------------------------------------- 24: Test Simple UFF molecule optimization, part 2. 24: done 24: ------------------------------------- 24: Test UFF Torsion Conflicts. 24: C 0.4783 -0.7477 -0.0753 24: C -0.5465 -0.0176 0.3519 24: C -0.5114 1.4472 0.0870 24: H -1.5201 -0.4838 0.2485 24: H 0.4696 1.8363 0.3367 24: O -1.2618 1.9423 0.6934 24: F -0.7163 1.6298 -0.9622 24: done 24: ------------------------------------- 24: Unit tests for UFF distance constraint terms. 24: done 24: ------------------------------------- 24: Unit tests for all UFF constraint terms. 24: done 24: ------------------------------------- 24: Unit tests for copying UFF ForceFields. 24: done 24: ------------------------------------- 24: Unit test for UFF butane scan. 1: cyclosporine a 1: RDKit 2D 1: 1: 85 85 0 0 0 0 0 0 0 0999 V2000 1: 1.4840 -0.8529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6174 -1.3521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6176 -2.3509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4860 -2.8479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4912 -3.8489 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.3504 -2.3385 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.3352 -1.3311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.1902 -0.7993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.1580 0.1961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.0642 -1.2607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.9260 -0.7295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.9144 0.3303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.7766 0.8337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.0008 0.8409 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.8596 1.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.8162 2.2071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2038 1.4219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2560 3.1855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5280 4.2325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7128 4.8927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.8530 5.8895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.7676 4.5077 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0820 5.0835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.9744 4.6151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.8344 5.1337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.9792 3.6203 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.8192 3.0813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.7974 3.5817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.7998 4.5809 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.7790 3.0789 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.8812 2.0705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.1202 1.6017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.4194 2.0931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.0590 0.6211 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.8626 0.0983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.8096 -0.8961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.6470 -1.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.9122 -1.3587 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.8776 -2.3565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9982 -2.8425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1382 -2.3311 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9886 -3.8459 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1202 -4.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2526 -3.8491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6116 -4.3521 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2494 -2.8505 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1228 -5.3475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2584 -5.8507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6092 -5.3541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2624 -6.8511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6018 -7.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5982 -8.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4624 -8.8579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9906 -5.8449 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.8520 -4.3501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.7288 -2.8719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.7098 -3.8701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.6032 -2.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.0646 -0.8235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.7362 0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5794 0.0605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5618 -0.9361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -6.4498 0.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.1626 0.1727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.7698 1.6253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5952 2.1745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -6.4896 1.7311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5292 3.1711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.6054 3.6407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.7186 2.0867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0328 6.0847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.4396 4.6417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.4580 5.6909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.3220 6.1985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5836 6.2065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2682 3.0557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.6630 2.5215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.5648 3.5065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.5876 2.1073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.7968 -1.2481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.6784 -0.7913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 7.5218 -1.3355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.7252 0.2017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.0970 -2.2659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.2220 -2.8307 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 3 2 1 1 1: 3 4 1 0 1: 4 5 2 0 1: 4 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 2 0 1: 8 10 1 0 1: 10 11 1 0 1: 11 12 1 0 1: 12 13 2 0 1: 12 14 1 0 1: 14 15 1 0 1: 15 16 1 0 1: 16 17 2 0 1: 16 18 1 0 1: 18 19 1 0 1: 19 20 1 0 1: 20 21 2 0 1: 20 22 1 0 1: 22 23 1 0 1: 23 24 1 0 1: 24 25 2 0 1: 24 26 1 0 1: 26 27 1 0 1: 27 28 1 0 1: 28 29 2 0 1: 28 30 1 0 1: 30 31 1 0 1: 31 32 1 0 1: 32 33 2 0 1: 32 34 1 0 1: 34 35 1 0 1: 35 36 1 0 1: 36 37 2 0 1: 36 38 1 0 1: 38 39 1 0 1: 39 40 1 0 1: 40 41 2 0 1: 40 42 1 0 1: 43 42 1 6 1: 43 44 1 0 1: 44 45 2 0 1: 44 46 1 0 1: 43 47 1 0 1: 47 48 1 0 1: 48 49 1 6 1: 48 50 1 0 1: 50 51 1 0 1: 51 52 2 0 1: 52 53 1 0 1: 47 54 1 1 1: 42 55 1 0 1: 39 56 1 6 1: 56 57 1 0 1: 56 58 1 0 1: 38 59 1 0 1: 35 60 1 6 1: 60 61 1 0 1: 61 62 1 0 1: 61 63 1 0 1: 34 64 1 0 1: 31 65 1 6 1: 65 66 1 0 1: 66 67 1 0 1: 66 68 1 0 1: 30 69 1 0 1: 27 70 1 6 1: 23 71 1 6 1: 19 72 1 6 1: 72 73 1 0 1: 73 74 1 0 1: 73 75 1 0 1: 18 76 1 0 1: 15 77 1 6 1: 77 78 1 0 1: 77 79 1 0 1: 11 80 1 6 1: 80 81 1 0 1: 81 82 1 0 1: 81 83 1 0 1: 10 84 1 0 1: 6 85 1 0 1: 46 3 1 0 1: M END 1: 1: single-double 1: RDKit 2D 1: 1: 17 16 0 0 0 0 0 0 0 0999 V2000 1: -6.9282 -0.2298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -6.0618 0.2696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.1962 -0.2312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.3298 0.2682 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.4642 -0.2326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.5978 0.2668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.7322 -0.2340 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8658 0.2654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0002 -0.2352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8662 0.2640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7318 -0.2366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5982 0.2626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.4638 -0.2380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.3302 0.2612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.1958 -0.2394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.0622 0.2598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.9278 -0.2408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 2 3 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 2 3 1: 11 12 1 0 1: 12 13 2 3 1: 13 14 1 0 1: 14 15 2 3 1: 15 16 1 0 1: 16 17 1 0 1: M END 1: 1: cis-trans 1: RDKit 2D 1: 1: 10 9 0 0 0 0 0 0 0 0999 V2000 1: -3.6370 -0.2028 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.7706 -0.7022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9050 -0.2016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.0386 -0.7008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1730 -0.2002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6934 -0.6994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5590 -0.1988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5582 0.8012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.4238 1.3020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.2902 0.8026 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 2 0 1: 3 4 1 0 1: 4 5 2 0 1: 5 6 1 0 1: 6 7 2 0 1: 7 8 1 0 1: 8 9 2 0 1: 9 10 1 0 1: M END 1: 1: admntn 1: RDKit 2D 1: 1: 10 12 0 0 0 0 0 0 0 0999 V2000 1: 1.3505 -0.5360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5267 -1.1020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4629 -1.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.7523 0.0052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4741 0.5660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4761 0.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3505 1.0730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.0611 0.5080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0643 0.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1877 -0.5490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 6 10 1 0 1: 8 1 1 0 1: 9 4 1 0 1: 10 2 1 0 1: M END 1: 1: github 4845 - nan coordinates but no crash 1: RDKit 2D 1: 1: 42 44 0 0 0 0 0 0 0 0999 V2000 1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 2 0 1: 4 5 1 0 1: 5 6 3 0 1: 6 7 1 0 1: 7 8 2 0 1: 8 9 1 0 1: 9 10 3 0 1: 10 11 1 0 1: 11 12 2 0 1: 12 13 1 0 1: 13 14 3 0 1: 14 15 1 0 1: 15 16 2 0 1: 16 17 1 0 1: 16 18 1 0 1: 12 19 1 0 1: 19 20 2 0 1: 20 21 1 0 1: 20 22 1 0 1: 19 23 1 0 1: 23 24 3 0 1: 24 25 1 0 1: 25 26 1 0 1: 26 27 2 0 1: 27 28 2 0 1: 26 29 1 0 1: 29 30 3 0 1: 8 31 1 0 1: 31 32 2 0 1: 32 33 1 0 1: 32 34 1 0 1: 31 35 1 0 1: 35 36 3 0 1: 36 37 1 0 1: 37 38 2 0 1: 37 39 1 0 1: 39 40 2 0 1: 40 41 1 0 1: 40 42 1 0 1: 39 4 1 0 1: 15 7 1 0 1: 30 11 1 0 1: M END 1: 14/222 Test #1: testCoordGen ........................... Passed 0.65 sec test 25 Start 25: testMMFFForceField 25: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/MMFF/testMMFFForceField 25: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/MMFF 25: Test timeout computed to be: 1500 25: ------------------------------------- 25: Official MMFF validation suite. 12: ...... 12: ---------------------------------------------------------------------- 12: Ran 6 tests in 0.005s 12: 12: OK 13: ......... 13: ---------------------------------------------------------------------- 13: Ran 9 tests in 0.015s 13: 13: OK 22: ..... 22: ---------------------------------------------------------------------- 22: Ran 5 tests in 0.003s 22: 22: OK 22: Testing Alignment Wrapper code: 14: ......... 14: ---------------------------------------------------------------------- 14: Ran 9 tests in 0.047s 14: 14: OK 15/222 Test #12: pyDiscreteValueVect .................... Passed 0.70 sec test 26 Start 26: pyForceFieldConstraints 26: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/ForceField/Wrap/testConstraints.py" 26: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/Wrap 26: Test timeout computed to be: 1500 16/222 Test #13: pySparseIntVect ........................ Passed 0.72 sec test 27 Start 27: testDistGeom 27: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom/testDistGeom 27: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom 27: Test timeout computed to be: 1500 18: ........... 18: ---------------------------------------------------------------------- 18: Ran 11 tests in 0.050s 18: 18: OK 18: Testing Geometry wrapper 17/222 Test #22: pyAlignment ............................ Passed 0.64 sec test 28 Start 28: pyDistGeom 28: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap/rough_test.py" 28: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom/Wrap 28: Test timeout computed to be: 1500 18/222 Test #14: pyFPB .................................. Passed 0.76 sec test 29 Start 29: graphmolTest1 29: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 29: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 29: Test timeout computed to be: 1500 27: *********************************************************** 27: test1 27: *********************************************************** 27: testIssue216 27: Rows: 4 Columns: 4 27: 0 1 1 1 27: 1 0 1 1 27: 1 1 0 1 27: 1 1 1 0 27: *********************************************************** 27: 19/222 Test #18: testPyGeometry ......................... Passed 0.72 sec test 30 Start 30: graphmolcpTest 30: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolcpTest 30: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 30: Test timeout computed to be: 1500 24: done 20/222 Test #24: testUFFForceField ...................... Passed 0.64 sec 21/222 Test #27: testDistGeom ........................... Passed 0.06 sec test 31 Start 31: graphmolqueryTest 31: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolqueryTest 31: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 31: Test timeout computed to be: 1500 test 32 Start 32: graphmolMolOpsTest 32: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolMolOpsTest 32: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 32: Test timeout computed to be: 1500 30: 30: 30: 30: COPY 31: [21:31:29] ---------------------- Test1 29: Atoms: 29: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 0 arom?: 0 chi: 0 29: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 29: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 0 arom?: 0 chi: 0 29: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 29: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 29: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 29: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: 0 arom?: 0 chi: 0 29: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: 0 arom?: 1 chi: 0 29: 8 22 Ti chg: 0 deg: 1 exp: [21:31:29] 29: 29: **** 29: Pre-condition Violation 29: getExplicitValence() called without call to calcExplicitValence() 29: Violation occurred on line 298 in file ./Code/GraphMol/Atom.cpp 29: Failed Expression: d_explicitValence > -1 29: **** 29: 29: N/A imp: -1 hyb: 0 arom?: 0 chi: 0 29: Bonds: 29: 0 0->1 order: 1 conj?: 0 aromatic?: 0 29: 1 1->2 order: 2 conj?: 0 aromatic?: 0 29: 2 2->3 order: 1 conj?: 0 aromatic?: 0 29: 3 0->4 order: 1 conj?: 0 aromatic?: 0 29: 4 5->6 order: 3 conj?: 0 aromatic?: 0 29: 5 6->7 order: 1 conj?: 0 aromatic?: 0 29: 6 7->8 order: 2 conj?: 0 aromatic?: 0 29: [21:31:29] 29: 29: **** 29: Pre-condition Violation 29: bond already exists 29: Violation occurred on line 380 in file ./Code/GraphMol/RWMol.cpp 29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 29: **** 29: 29: [21:31:29] 29: 29: **** 29: Pre-condition Violation 29: bond already exists 29: Violation occurred on line 380 in file ./Code/GraphMol/RWMol.cpp 29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 29: **** 29: 29: [21:31:29] 29: 29: **** 29: Pre-condition Violation 29: attempt to add self-bond 29: Violation occurred on line 379 in file ./Code/GraphMol/RWMol.cpp 29: Failed Expression: atomIdx1 != atomIdx2 29: **** 29: 29: [21:31:29] 29: 29: **** 29: Pre-condition Violation 29: bond already exists 29: Violation occurred on line 441 in file ./Code/GraphMol/ROMol.cpp 29: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) 29: **** 29: 29: [21:31:29] 29: 29: **** 29: Pre-condition Violation 29: attempt to add self-bond 29: Violation occurred on line 439 in file ./Code/GraphMol/ROMol.cpp 29: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() 29: **** 29: 29: [21:31:29] Explicit valence for atom # 0 B, 4, is greater than permitted 29: [21:31:29] Explicit valence for atom # 0 B, 5, is greater than permitted 22/222 Test #30: graphmolcpTest ......................... Passed 0.03 sec test 33 Start 33: graphmoltestChirality 33: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmoltestChirality 33: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 33: Test timeout computed to be: 1500 31: [21:31:29] Done! 31: [21:31:29] ---------------------- Test2 31: [21:31:29] Done! 31: [21:31:29] ---------------------- Test3 31: [21:31:29] Done! 31: [21:31:29] ---------------------- Test4 31: [21:31:29] Done! 31: [21:31:29] ---------------------- Test5 31: [21:31:29] Done! 31: [21:31:29] Done! 31: [21:31:29] ---------------------- Test issue 2892580 31: [21:31:29] Done! 31: [21:31:29] ---------------------- Test github issue 53: query molecules not matching [R] 31: [21:31:29] Done! 31: [21:31:29] ---------------------- Test queries using qualifiers instead of == 31: [21:31:29] Done! 31: [21:31:29] ---------------------- Test Github issue 165: radicals not used in atom-atom matching 31: [21:31:29] Done! 31: [21:31:29] ---------------------- Test extra atom queries 31: [21:31:29] Done! 31: [21:31:29] ---------------------- Test extra bond queries 31: [21:31:29] Done! 31: [21:31:29] ---------------------- Test num heteroatom neighbor queries 31: [21:31:29] Done! 31: [21:31:29] ---------------------- Test atom type queries 31: [21:31:29] Done! 31: [21:31:29] ---------------------- Test Github #2471: dummy atom queries are flagged as complex 31: [21:31:29] Done! 31: [21:31:29] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() 31: [21:31:29] Done! 23/222 Test #2: pyCoordGen .............................***Exception: SegFault 0.88 sec 24/222 Test #31: graphmolqueryTest ...................... Passed 0.04 sec test 34 Start 34: graphmoltestPickler 34: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmoltestPickler 34: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 34: Test timeout computed to be: 1500 test 35 Start 35: graphmoltestPicklerGlobalSetting 35: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting 35: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 35: Test timeout computed to be: 1500 29: [21:31:29] 29: 29: **** 29: Post-condition Violation 29: Element 'Xx' not found 29: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 29: Failed Expression: anum > -1 29: **** 29: 29: [21:31:29] ------------------------------------- 29: [21:31:29] Test github381: thread-safe initialization of the periodic table 25: 25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... 29: [21:31:29] done 29: [21:31:29] ------------------------------------- 29: [21:31:29] Test github1041: Segfault for atom with no owner (expect some warnings) 29: [21:31:29] 29: 29: **** 29: Pre-condition Violation 29: no owner 29: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 29: Failed Expression: dp_mol 29: **** 29: 29: [21:31:29] 29: 29: **** 29: Pre-condition Violation 29: no owner 29: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h 29: Failed Expression: dp_mol 29: **** 29: 29: [21:31:29] done 29: [21:31:29] ------------------------------------- 29: [21:31:29] Test github1041: Segfault for atom with no owner (expect some warnings) 29: [21:31:29] 29: 29: **** 29: Pre-condition Violation 29: no owner 29: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 29: Failed Expression: dp_mol 29: **** 29: 29: [21:31:29] 29: 29: **** 29: Pre-condition Violation 29: no owner 29: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h 29: Failed Expression: dp_mol 29: **** 29: 29: [21:31:29] done 29: [21:31:29] ------------------------------------- 29: [21:31:29] Test github1453: RWMol.clear() should reset the numBonds count. 29: [21:31:29] done 29: [21:31:29] ------------------------------------- 29: [21:31:29] Test range-based for loops. 29: [21:31:29] done 29: [21:31:29] ------------------------------------- 29: [21:31:29] Test github1642: Atom index type is too low for big molecules. 34: [21:31:29] ------------------------------------- 34: [21:31:29] Testing String Pickle Roundtrips. 33: -------------------------- 33: -------------------------- 33: C/C=C/C(C)Cl 3: dynamic boost any:0.660763 s 35: [21:31:30] done 25/222 Test #35: graphmoltestPicklerGlobalSetting ....... Passed 0.06 sec test 36 Start 36: graphmolIterTest 36: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolIterTest 36: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 36: Test timeout computed to be: 1500 32: 1 1 2 32: 1 1 1 32: 2 1 0.75 32: path: 2 32: [21:31:30] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored 32: [21:31:30] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 13 ignored 32: [21:31:30] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored 32: [21:31:30] Explicit valence for atom # 0 B, 5, is greater than permitted 32: [21:31:30] Explicit valence for atom # 1 C, 5, is greater than permitted 32: [21:31:30] Explicit valence for atom # 1 C, 5, is greater than permitted 32: [21:31:30] Explicit valence for atom # 1 C, 5, is greater than permitted 32: [21:31:30] Explicit valence for atom # 1 Si, 7, is greater than permitted 26/222 Test #36: graphmolIterTest ....................... Passed 0.06 sec test 37 Start 37: hanoiTest 37: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/hanoiTest 37: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 37: Test timeout computed to be: 1500 3: static RDAny:0.09474 s 33: [21:31:30] Conflicting single bond directions around double bond at index 2. 33: [21:31:30] BondStereo set to STEREONONE and single bond directions set to NONE. 33: [21:31:30] Conflicting single bond directions around double bond at index 4. 33: [21:31:30] BondStereo set to STEREONONE and single bond directions set to NONE. 33: [21:31:30] Conflicting single bond directions around double bond at index 15. 33: [21:31:30] BondStereo set to STEREONONE and single bond directions set to NONE. 33: [21:31:30] Conflicting single bond directions around double bond at index 2. 33: [21:31:30] BondStereo set to STEREONONE and single bond directions set to NONE. 33: [21:31:30] Conflicting single bond directions around double bond at index 1. 33: [21:31:30] BondStereo set to STEREONONE and single bond directions set to NONE. 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing reading existing pickle file (v2). 33: -------------------------------------------------- 27/222 Test #26: pyForceFieldConstraints ................***Exception: SegFault 0.35 sec 28/222 Test #33: graphmoltestChirality .................. Passed 0.25 sec test 38 Start 38: graphmolMemTest1 38: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolMemTest1 38: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 38: Test timeout computed to be: 1500 test 39 Start 39: resMolSupplierTest 39: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/resMolSupplierTest 39: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 39: Test timeout computed to be: 1500 28: ...... 28: ---------------------------------------------------------------------- 28: Ran 6 tests in 0.001s 28: 28: OK 29/222 Test #38: graphmolMemTest1 ....................... Passed 0.02 sec test 40 Start 40: molBundleTest 40: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/molBundleTest 40: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 40: Test timeout computed to be: 1500 32: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing combining molecules using pickles. 34: Atoms: 34: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 34: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 34: 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 34: 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 34: 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 34: 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 4 arom?: 0 chi: 0 34: 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 34: Bonds: 34: 0 0->1 order: 1 conj?: 0 aromatic?: 0 34: 1 1->2 order: 1 conj?: 0 aromatic?: 0 34: 2 2->0 order: 1 conj?: 0 aromatic?: 0 34: 3 3->4 order: 1 conj?: 0 aromatic?: 0 34: 4 4->5 order: 1 conj?: 0 aromatic?: 0 34: 5 5->6 order: 1 conj?: 0 aromatic?: 0 34: 6 6->3 order: 1 conj?: 0 aromatic?: 0 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing Issue164: Roundtrip Pickle Failure. 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing Issue219: Pickle Failure with Conformations. 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing Issue220: Pickle problems with bond stereochemistry. 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing query serialization. 34: [21:31:30] C=[$(C=O)] 34: [21:31:30] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing radical handling in pickles. 34: [21:31:30] done 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing sf.net issue 2788233. 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing sf.net issue 3202580. 34: mass! 13.0034 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing sf.net issue 3316407. 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing sf.net issue 3496759. 34: smi match: *C *C 34: smi match: **=* **=* 34: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O 30/222 Test #28: pyDistGeom ............................. Passed 0.37 sec test 41 Start 41: testSGroup 41: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/testSGroup 41: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 41: Test timeout computed to be: 1500 34: smi match: *OS(=O)OC *OS(=O)OC 34: smi match: *S(=O)(=O)OC *S(=O)(=O)OC 34: smi match: O=COC=O O=COC=O 34: smi match: OO OO 34: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 34: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 34: smi match: nnnOC=O nnnOC=O 34: smi match: *=C=N *=C=N 34: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F 34: smi match: SP(S)=S SP(S)=S 34: smi match: NP(N)(N)=O NP(N)(N)=O 34: smi match: cN=[N+]=[N-] cN=[N+]=[N-] 34: smi match: *CC=O *CC=O 34: smi match: NNC=O NNC=O 34: smi match: * * 34: smi match: C=P C=P 34: smi match: CC(=N)Cl CC(=N)Cl 34: smi match: N=O N=O 34: smi match: ** ** 34: smi match: N=C=N N=C=N 34: smi match: [C-]#[NH+] [C-]#[NH+] 34: smi match: O=CON(C=O)C=O O=CON(C=O)C=O 34: smi match: N#CC[OH] N#CC[OH] 34: smi match: N#CC=O N#CC=O 34: smi match: N#CS(=O)=O N#CS(=O)=O 34: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC 34: smi match: N#CN=N N#CN=N 34: smi match: N=NCC=O N=NCC=O 34: smi match: CCCCCCC CCCCCCC 34: smi match: OCCOCCO OCCOCCO 34: smi match: SS SS 34: smi match: [SH] [SH] 34: smi match: *1CC1 *1CC1 34: smi match: [OH]ccc([OH])c[OH] [OH]ccc([OH])c[OH] 34: smi match: [OH]cc([OH])c[OH] [OH]cc([OH])c[OH] 31/222 Test #40: molBundleTest .......................... Passed 0.05 sec test 42 Start 42: test-valgrind 42: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/test-valgrind 42: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 42: Test timeout computed to be: 1500 34: smi match: NC(=S)N=N NC(=S)N=N 34: smi match: N#CS N#CS 34: smi match: cC[N+] cC[N+] 34: smi match: C*C=S C*C=S 34: smi match: N[CH2]C#N N[CH2]C#N 34: smi match: O=C1CCO1 O=C1CCO1 34: smi match: O=P([OH])OP(=O)[OH] O=P([OH])OP(=O)[OH] 34: smi match: O=C1CCN1 O=C1CCN1 34: smi match: O=C1C~CC(=O)C~C1 O=C1C~CC(=O)C~C1 34: smi match: C=CC=CC=CC=C C=CC=CC=CC=C 34: smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1 34: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 34: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 34: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 34: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 34: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 34: smi match: cN(=O)~O cN(=O)~O 34: smi match: *[CH2]N1C(=O)CCC1=O *[CH2]N1C(=O)CCC1=O 34: smi match: N~NC=O N~NC=O 34: smi match: *=N~C *=N~C 34: smi match: CO*(=O)=O CO*(=O)=O 34: smi match: * * 34: smi match: * * 34: smi match: *C=C *C=C 34: smi match: N#CS N#CS 34: smi match: *C=S *C=S 34: smi match: *N *N 34: smi match: *C(=C)C=O *C(=C)C=O 34: smi match: *C#C *C#C 34: smi match: N#CCO N#CCO 34: smi match: O=N(=O)CCO O=N(=O)CCO 34: smi match: N=CS N=CS 34: smi match: O=CNC(O)C=O O=CNC(O)C=O 34: smi match: C=C(C=O)C=O C=C(C=O)C=O 34: smi match: N=CC=O N=CC=O 34: smi match: *C(C=O)C=O *C(C=O)C=O 34: smi match: *C(C=O)=C(*)C=O *C(C=O)=C(*)C=O 34: smi match: O=CC=CC=O O=CC=CC=O 34: smi match: O=CN(O)C=O O=CN(O)C=O 34: smi match: O=CN(S)C=O O=CN(S)C=O 34: smi match: O=CNC=O O=CNC=O 34: smi match: O=CNN=O O=CNN=O 34: smi match: O=CNNC=O O=CNNC=O 32: [21:31:30] non-ring atom 0 marked aromatic 32: [21:31:30] non-ring atom 0 marked aromatic 34: smi match: O=CNOC=O O=CNOC=O 34: smi match: O=CS O=CS 34: smi match: O=CSC=S O=CSC=S 34: smi match: S=CS S=CS 34: smi match: C=O C=O 34: smi match: *C=N *C=N 34: smi match: CCCCCCC CCCCCCC 34: smi match: CN=O CN=O 34: smi match: CS(=O)(=O)O CS(=O)(=O)O 34: smi match: O=C1CCO1 O=C1CCO1 34: smi match: C=C(S)[SH]=O C=C(S)[SH]=O 34: smi match: C=CCO C=CCO 34: smi match: C=CC=N C=CC=N 34: smi match: C=CC=O C=CC=O 34: smi match: C=CC(=O)C=C C=CC(=O)C=C 34: smi match: C=CC=S C=CC=S 34: smi match: C=CC(=S)S C=CC(=S)S 34: smi match: *C=C(*)C=C *C=C(*)C=C 34: smi match: C=CC=N C=CC=N 34: smi match: *N(*)C=C *N(*)C=C 34: smi match: C=CN(=O)=O C=CN(=O)=O 34: smi match: C=CN(O)=O C=CN(O)=O 34: smi match: C=CO C=CO 34: smi match: C=COC=O C=COC=O 34: smi match: C=CS C=CS 34: smi match: C=C[SH](=O)=O C=C[SH](=O)=O 34: smi match: C=NCO C=NCO 34: smi match: C=NC=O C=NC=O 34: smi match: C=NN C=NN 32: [21:31:30] Conflicting single bond directions around double bond at index 17. 32: [21:31:30] BondStereo set to STEREONONE and single bond directions set to NONE. 34: smi match: C=NN=C C=NN=C 34: smi match: C=NO C=NO 34: smi match: C=NOC=O C=NOC=O 34: smi match: C=N=O C=N=O 34: smi match: N#CS N#CS 34: smi match: *CN=O *CN=O 34: smi match: NCN NCN 34: smi match: ON=CCN=O ON=CCN=O 34: smi match: NC(S)=N[SH](=O)=O NC(S)=N[SH](=O)=O 34: smi match: N=C(N)S N=C(N)S 34: smi match: NC(=O)Oc1ccccc1 NC(=O)Oc1ccccc1 34: smi match: NC=S NC=S 34: smi match: NC(N)=S NC(N)=S 34: smi match: C=CN C=CN 34: smi match: NOC=O NOC=O 34: smi match: C1CN1 C1CN1 34: smi match: O=C1NNNN1 O=C1NNNN1 34: smi match: N=C(N)C(=N)N N=C(N)C(=N)N 34: smi match: N=C(N)O N=C(N)O 34: smi match: N=C(N)C(=N)S N=C(N)C(=N)S 34: smi match: *C=N *C=N 34: smi match: N=CC=O N=CC=O 34: smi match: N=CS N=CS 34: smi match: N=C=N N=C=N 34: smi match: N=C=O N=C=O 34: smi match: N=C=S N=C=S 34: smi match: NOC(=O)O NOC(=O)O 34: smi match: *C(O)=S *C(O)=S 34: smi match: C=CO C=CO 34: smi match: ON=CC=NO ON=CC=NO 34: smi match: *C[SH](=O)=O *C[SH](=O)=O 34: smi match: OS(=O)=O OS(=O)=O 34: smi match: N#CS N#CS 34: smi match: C=C(S)S C=C(S)S 34: smi match: N=C(N)S N=C(N)S 34: smi match: N=C(S)S N=C(S)S 32: starting ring finding 32: done 32: starting ring finding 32: done 32: starting ring finding 34: smi match: NC(=S)S NC(=S)S 34: smi match: O=CNS O=CNS 34: smi match: S S 34: smi match: [SiH4] [SiH4] 34: smi match: NS NS 34: smi match: NCN NCN 34: smi match: cC(c)(O)O cC(c)(O)O 34: smi match: *C(c)O *C(c)O 34: smi match: C=CS(c)(=O)=O C=CS(c)(=O)=O 34: smi match: cS(=O)(=O)O cS(=O)(=O)O 34: smi match: *c1ccccn1=O *c1ccccn1=O 34: smi match: *c1ccccn1 *c1ccccn1 34: smi match: *c1nccccn1 *c1nccccn1 34: smi match: C1COCOC1 C1COCOC1 34: smi match: C=S C=S 34: smi match: c=S c=S 34: smi match: S=CS S=CS 34: smi match: C=CN(=O)=O C=CN(=O)=O 34: smi match: C=CN(=O)O C=CN(=O)O 34: smi match: N=CC=O N=CC=O 34: smi match: C=CS C=CS 34: smi match: SC(S)(S)S SC(S)(S)S 34: smi match: OS(O)(O)O OS(O)(O)O 34: smi match: O=N(=O)C[SH](=O)=O O=N(=O)C[SH](=O)=O 34: smi match: O=N(O)C[SH](=O)=O O=N(O)C[SH](=O)=O 32: done 32: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C 32: starting sanitization 34: smi match: N#CS N#CS 34: smi match: C=NO C=NO 34: smi match: C=N[SH]=N C=N[SH]=N 34: smi match: O=C(S)S O=C(S)S 34: smi match: N=C(S)S N=C(S)S 34: smi match: N=C(=N)S N=C(=N)S 34: smi match: O=N=O O=N=O 34: smi match: O=NO O=NO 34: smi match: ONO ONO 34: smi match: C1SCS1 C1SCS1 34: smi match: N=C=S N=C=S 34: smi match: N=C=N N=C=N 34: smi match: C1N=N1 C1N=N1 34: smi match: *CS *CS 34: smi match: SC(S)=C(S)S SC(S)=C(S)S 34: smi match: N=CC=NO N=CC=NO 34: smi match: N#CCC#N N#CCC#N 34: smi match: CON=O CON=O 34: smi match: C=CN C=CN 34: smi match: C=N[SH](=O)=O C=N[SH](=O)=O 34: smi match: NN=O NN=O 34: smi match: NC(=O)S NC(=O)S 34: smi match: N#CS N#CS 34: smi match: NC(=O)C(N)=O NC(=O)C(N)=O 34: smi match: c=N c=N 34: smi match: C1COCO1 C1COCO1 34: smi match: C=NN[SH](=O)=O C=NN[SH](=O)=O 34: smi match: O=CC=O O=CC=O 34: smi match: O=CNOC=O O=CNOC=O 34: smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 34: smi match: ONO ONO 34: smi match: ON(~O)~O ON(~O)~O 34: smi match: OC1COC(O)C1 OC1COC(O)C1 34: smi match: OC1CCOC1O OC1CCOC1O 34: smi match: OC1CCOC(O)C1 OC1CCOC(O)C1 34: smi match: N=[N+]=N N=[N+]=N 34: smi match: N#CN N#CN 34: smi match: C=NN=C C=NN=C 34: smi match: *CCN(C)C *CCN(C)C 34: smi match: CNN CNN 34: smi match: *CC *CC 34: smi match: OCS OCS 34: smi match: C1NO1 C1NO1 34: smi match: COS(C)(=O)=O COS(C)(=O)=O 34: smi match: C1CO1 C1CO1 34: smi match: *c1-c-c-ccN1 *c1-c-c-ccN1 34: smi match: *C(*)=C *C(*)=C 34: smi match: N#[NH+] N#[NH+] 34: smi match: C#NO C#NO 34: smi match: OOO OOO 34: smi match: OO OO 34: smi match: O~Cl(~O)~O O~Cl(~O)~O 34: smi match: O~Cl(~O)(~O)~O O~Cl(~O)(~O)~O 34: smi match: [OH]~C(~O)~O [OH]~C(~O)~O 34: smi match: *N *N 32/222 Test #42: test-valgrind .......................... Passed 0.06 sec test 43 Start 43: graphmolTestsCatch 43: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch 43: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 43: Test timeout computed to be: 1500 34: smi match: *P *P 34: smi match: *S *S 34: smi match: *C(*)(*)C=C *C(*)(*)C=C 34: smi match: *C(*)(*)C=C *C(*)(*)C=C 34: smi match: *C(*)C=C *C(*)C=C 34: smi match: *CC=C *CC=C 34: smi match: CN=C=O CN=C=O 34: smi match: CN=C=S CN=C=S 34: smi match: *C=O *C=O 34: smi match: N=N N=N 34: smi match: SS SS 34: smi match: O=C1CCNC(=O)O1 O=C1CCNC(=O)O1 34: smi match: CSC(C)=N CSC(C)=N 34: smi match: COC(C)=N COC(C)=N 34: smi match: C=C=C C=C=C 34: smi match: *C(=O)OC=O *C(=O)OC=O 34: smi match: C=CC#N C=CC#N 34: smi match: C=CC=O C=CC=O 34: smi match: CC=CC(C)=O CC=CC(C)=O 34: smi match: CC=CC(=O)OCC CC=CC(=O)OCC 34: smi match: C#CC#N C#CC#N 34: smi match: C#CC=O C#CC=O 34: smi match: C#CC(=O)OCC C#CC(=O)OCC 34: smi match: C#CC=O C#CC=O 34: smi match: *C(=O)C#C *C(=O)C#C 34: smi match: C=CC=O C=CC=O 34: smi match: *C(*)(*)O *C(*)(*)O 34: smi match: COS(O)(=O)=O COS(O)(=O)=O 34: smi match: CS(=O)(=O)[O-] CS(=O)(=O)[O-] 34: smi match: NS(=O)(=O)[O-] NS(=O)(=O)[O-] 34: smi match: *C(*)(*)C=O *C(*)(*)C=O 32: done 32: starting sanitization 34: smi match: *C(*)(*)C=O *C(*)(*)C=O 34: smi match: *C(*)C=O *C(*)C=O 34: smi match: *CC=O *CC=O 34: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 34: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 34: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O 34: smi match: *C[SH](=O)=O *C[SH](=O)=O 32: done 34: smi match: * * 34: smi match: *1CC1 *1CC1 34: smi match: O=COC=O O=COC=O 34: smi match: N=C=O N=C=O 34: smi match: N=C=S N=C=S 34: smi match: O~O O~O 34: smi match: N~[SiH4] N~[SiH4] 34: smi match: *P *P 34: smi match: C=N=N C=N=N 34: smi match: *N#[NH+] *N#[NH+] 32: starting ring finding 32: done 32: starting ring finding 32: done 32: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 34: smi match: *S* *S* 34: smi match: ** ** 34: smi match: *CC* *CC* 34: smi match: *O[SiH3] *O[SiH3] 34: smi match: *OS(*)~O *OS(*)~O 34: smi match: N~N~O N~N~O 34: smi match: *N(~O)(~O)~O *N(~O)(~O)~O 34: smi match: *[N+](=C)[O-] *[N+](=C)[O-] 34: smi match: * * 34: smi match: *C(*)NCN(*)* *C(*)NCN(*)* 34: smi match: *OCC#N *OCC#N 34: smi match: **C=C **C=C 34: smi match: C=C[O-] C=C[O-] 34: smi match: C=CO C=CO 34: smi match: * * 34: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O 34: smi match: O=COn1ccnc1 O=COn1ccnc1 34: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 34: smi match: CC(C)(C)S CC(C)(C)S 33/222 Test #41: testSGroup ............................. Passed 0.10 sec test 44 Start 44: graphmolOrganometallicsCatch 44: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch 44: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 44: Test timeout computed to be: 1500 34: smi match: [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C 34: smi match: [CH]=O [CH]=O 34: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C 34: smi match: SS SS 34: smi match: [SH] [SH] 34: smi match: *C* *C* 34: smi match: * * 34: smi match: C[nH3+] C[nH3+] 34: smi match: cC(=N)[NH2] cC(=N)[NH2] 34: smi match: O=CN[OH] O=CN[OH] 34: smi match: NN NN 34: smi match: * * 34: smi match: *OP(=O)O* *OP(=O)O* 34: smi match: * * 34: smi match: * * 34: smi match: * * 34: smi match: *N=C(*)* *N=C(*)* 34: smi match: *C(*)(*)C=O *C(*)(*)C=O 34: smi match: CSC=O CSC=O 34: smi match: * * 34: smi match: O=CCl O=CCl 34: smi match: *** *** 34: smi match: *C=O *C=O 34: smi match: C[OH] C[OH] 34: smi match: C[OH] C[OH] 34: smi match: C[OH] C[OH] 34: smi match: C[OH] C[OH] 34: smi match: C[CH]=O C[CH]=O 34: smi match: *=* *=* 34: smi match: *C *C 34: smi match: C#C C#C 34: smi match: *[CH]C=C *[CH]C=C 34: smi match: cCC(=O)[OH] cCC(=O)[OH] 34: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] 34: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] 34: smi match: C=CC(=O)[OH] C=CC(=O)[OH] 34: smi match: N#CC(=O)[OH] N#CC(=O)[OH] 34: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O 34: smi match: *N(*)C*=O *N(*)C*=O 34: smi match: O=*C[OH] O=*C[OH] 32: [21:31:30] WARNING: not removing hydrogen atom with dummy atom neighbors 32: ------------------------------- 32: [21:31:30] Explicit valence for atom # 0 N, 4, is greater than permitted 34: smi match: *=C*=O *=C*=O 34: smi match: *=CC#N *=CC#N 34: smi match: *C[OH] *C[OH] 34: smi match: ** ** 34: smi match: *C[OH] *C[OH] 34: smi match: *C(*)=O *C(*)=O 34: smi match: * * 34: smi match: *CC(=O)[OH] *CC(=O)[OH] 34: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O 34: smi match: *c *c 34: smi match: CN(C)c CN(C)c 34: smi match: c c 34: smi match: *c *c 34: smi match: *c *c 34: smi match: **:*cF **:*cF 34: smi match: cB([OH])[OH] cB([OH])[OH] 34: smi match: N~N~N N~N~N 34: smi match: *N=N* *N=N* 34: smi match: *CC[OH] *CC[OH] 34: smi match: *CC[OH] *CC[OH] 34: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] 34: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] 34: smi match: *CCC(=O)[OH] *CCC(=O)[OH] 34: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] 34: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O 34: smi match: *OC(*)=O *OC(*)=O 34: smi match: *C(=O)[OH] *C(=O)[OH] 34: smi match: O=C[OH] O=C[OH] 34: smi match: *OC(=O)O* *OC(=O)O* 34: smi match: * * 34: smi match: *OC(=O)Cl *OC(=O)Cl 34: smi match: *C#N *C#N 34: smi match: NCC(=O)NCC=O NCC(=O)NCC=O 34: smi match: SS SS 34: smi match: * * 34: smi match: *=* *=* 34: smi match: *=* *=* 34: smi match: *=* *=* 34: smi match: *=* *=* 34: smi match: C1CO1 C1CO1 34: smi match: *OC(*)=O *OC(*)=O 34: smi match: * * 34: smi match: *O*[OH] *O*[OH] 34: smi match: COC(C)(C)O COC(C)(C)O 34: smi match: *[OH] *[OH] 34: smi match: ** ** 34: smi match: C=N[NH2] C=N[NH2] 34: smi match: C=NC=O C=NC=O 34: smi match: * * 34: smi match: C#NC C#NC 34: smi match: CN=C=O CN=C=O 34: smi match: CN=C=S CN=C=S 34: smi match: *OC(*)(*)O* *OC(*)(*)O* 34: smi match: *C(*)=O *C(*)=O 34: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C 34: smi match: *~*=O *~*=O 34: smi match: *~*=O *~*=O 34: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] 34: smi match: * * 34: smi match: *C#N *C#N 34: smi match: *N(=O)~O *N(=O)~O 34: smi match: N N 34: smi match: OC(=O)C(O)=O OC(=O)C(O)=O 34: smi match: C=NO C=NO 34: smi match: O~O O~O 34: smi match: c[OH] c[OH] 34: smi match: O=P(~[OH])~O O=P(~[OH])~O 34: smi match: CO~P(=O)~O CO~P(=O)~O 34: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O 34: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O 34: smi match: O=P(~O)~O O=P(~O)~O 34: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O 34: smi match: C[NH2] C[NH2] 34: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 34: smi match: * * 34: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 34: smi match: CS(C)~O CS(C)~O 34: smi match: CS(C)(~O)~O CS(C)(~O)~O 34: smi match: CS(N)(~O)~O CS(N)(~O)~O 34: smi match: CS([OH])(~O)~O CS([OH])(~O)~O 34: smi match: COS(C)(~O)~O COS(C)(~O)~O 34: smi match: *S(C)(~O)~O *S(C)(~O)~O 34: smi match: CN(C)C CN(C)C 34: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 34: smi match: *C(*)=S *C(*)=S 34: smi match: *OC(*)=S *OC(*)=S 34: smi match: * * 34: smi match: C[SH] C[SH] 34: smi match: c[SH] c[SH] 34: smi match: NC(N)=S NC(N)=S 34: smi match: * * 34: smi match: ***** ***** 34: smi match: NC(N)=O NC(N)=O 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing sf.net issue 280. 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing sf.net issue 285. 34: [21:31:30] done 34: [21:31:30] done 34: [21:31:30] done 34: [21:31:30] done 34: [21:31:30] done 34: [21:31:30] done 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing Github2441: Add RDProps interface to Conformers. 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing Issue2510: Pickle Confs as double. 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing Github #2465: Negative atom-map numbers cause depickling to fail. 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing loading pickled mols with conformers 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing conformer reading/writing options 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing property reading options 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing property reading options 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing boost::serialization integration 34: [21:31:30] done 34: [21:31:30] ------------------------------------- 34: [21:31:30] Testing github issue 6036 32: [21:31:30] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 32: [21:31:30] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 32: [21:31:30] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 32: [21:31:30] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 34/222 Test #34: graphmoltestPickler .................... Passed 0.47 sec test 45 Start 45: graphmolSGroupCatch 45: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolSGroupCatch 45: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 45: Test timeout computed to be: 1500 32: [21:31:30] WARNING: not removing hydrogen atom with dummy atom neighbors 43: Randomness seeded to: 410672111 43: [21:31:30] WARNING: not removing hydrogen atom without neighbors 43: [21:31:30] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 43: [21:31:30] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 43: [21:31:30] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 43: [21:31:30] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 43: [21:31:30] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 43: [21:31:30] Explicit valence for atom # 1 N, 5, is greater than permitted 43: [21:31:30] Explicit valence for atom # 1 N, 6, is greater than permitted 43: [21:31:30] Explicit valence for atom # 1 N, 5, is greater than permitted 43: [21:31:30] Explicit valence for atom # 1 N, 5, is greater than permitted 43: [21:31:30] Explicit valence for atom # 2 O, 3, is greater than permitted 43: [21:31:30] Explicit valence for atom # 2 O, 3, is greater than permitted 43: [21:31:30] non-ring atom 2 marked aromatic 43: [21:31:30] non-ring atom 2 marked aromatic 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 1 2 3 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 1 2 3 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 0 1 2 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 0 1 2 43: [21:31:30] Explicit valence for atom # 1 O, 3, is greater than permitted 43: [21:31:30] Explicit valence for atom # 4 F, 2, is greater than permitted 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 6 7 8 43: [21:31:30] Explicit valence for atom # 1 C, 5, is greater than permitted 43: [21:31:30] WARNING: not removing hydrogen atom with dummy atom neighbors 43: [21:31:30] WARNING: not removing hydrogen atom with dummy atom neighbors 43: [21:31:30] WARNING: not removing hydrogen atom with wedged bond 43: [21:31:30] WARNING: not removing hydrogen atom without neighbors 43: [21:31:30] WARNING: not removing hydrogen atom without neighbors 43: [21:31:30] WARNING: not removing hydrogen atom without neighbors 43: [21:31:30] WARNING: not removing hydrogen atom without neighbors 43: [21:31:30] Unreasonable formal charge on hydrogen # 0. 43: [21:31:30] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() 43: [21:31:30] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() 43: [21:31:30] 43: 43: **** 43: Pre-condition Violation 43: no atom 43: Violation occurred on line 185 in file ./Code/GraphMol/ROMol.cpp 43: Failed Expression: at 43: **** 43: 43: [21:31:30] 43: 43: **** 43: Pre-condition Violation 43: no owner 43: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 43: Failed Expression: dp_mol 43: **** 43: 43: [21:31:30] 43: 43: **** 43: Pre-condition Violation 43: atom not associated with this molecule 43: Violation occurred on line 186 in file ./Code/GraphMol/ROMol.cpp 43: Failed Expression: &at->getOwningMol() == this 43: **** 43: 43: [21:31:30] 43: 43: **** 43: Pre-condition Violation 43: no atom 43: Violation occurred on line 385 in file ./Code/GraphMol/ROMol.cpp 43: Failed Expression: at 43: **** 43: 43: [21:31:30] 43: 43: **** 43: Pre-condition Violation 43: no owner 43: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 43: Failed Expression: dp_mol 43: **** 43: 43: [21:31:30] 43: 43: **** 43: Pre-condition Violation 43: atom not associated with this molecule 43: Violation occurred on line 386 in file ./Code/GraphMol/ROMol.cpp 43: Failed Expression: &at->getOwningMol() == this 43: **** 43: 43: [21:31:30] 43: 43: **** 43: Pre-condition Violation 43: no atom 43: Violation occurred on line 392 in file ./Code/GraphMol/ROMol.cpp 43: Failed Expression: at 43: **** 43: 43: [21:31:30] 43: 43: **** 43: Pre-condition Violation 43: no owner 43: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 43: Failed Expression: dp_mol 43: **** 43: 43: [21:31:30] 43: 43: **** 43: Pre-condition Violation 43: atom not associated with this molecule 43: Violation occurred on line 393 in file ./Code/GraphMol/ROMol.cpp 43: Failed Expression: &at->getOwningMol() == this 43: **** 43: 43: [21:31:30] 43: 43: **** 43: Pre-condition Violation 43: null atom passed in 43: Violation occurred on line 407 in file ./Code/GraphMol/ROMol.cpp 43: Failed Expression: atom_pin 43: **** 43: 43: [21:31:30] 43: 43: **** 43: Pre-condition Violation 43: cannot take ownership of an atom which already has an owner 43: Violation occurred on line 408 in file ./Code/GraphMol/ROMol.cpp 43: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this 43: **** 43: 44: Randomness seeded to: 2563671260 44: =============================================================================== 44: All tests passed (62 assertions in 6 test cases) 44: 43: [21:31:30] 43: 43: **** 43: Pre-condition Violation 43: cannot take ownership of an bond which already has an owner 43: Violation occurred on line 434 in file ./Code/GraphMol/ROMol.cpp 43: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this 43: **** 43: 43: [21:31:30] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 43: [21:31:30] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 43: [21:31:30] WARNING: not removing hydrogen atom without neighbors 43: [21:31:30] Explicit valence for atom # 1 F greater than permitted 43: [21:31:30] 43: 43: **** 43: Pre-condition Violation 43: plain atoms have no Query 43: Violation occurred on line 610 in file ./Code/GraphMol/Atom.cpp 43: Failed Expression: 0 43: **** 43: 43: [21:31:30] 43: 43: **** 43: Pre-condition Violation 43: plain atoms have no Query 43: Violation occurred on line 615 in file ./Code/GraphMol/Atom.cpp 43: Failed Expression: 0 43: **** 43: 43: [21:31:30] 43: 43: **** 43: Pre-condition Violation 43: plain bonds have no Query 43: Violation occurred on line 206 in file ./Code/GraphMol/Bond.cpp 43: Failed Expression: 0 43: **** 43: 43: [21:31:30] 43: 43: **** 43: Pre-condition Violation 43: plain bonds have no query 43: Violation occurred on line 227 in file ./Code/GraphMol/Bond.cpp 43: Failed Expression: 0 43: **** 43: 35/222 Test #44: graphmolOrganometallicsCatch ........... Passed 0.13 sec test 46 Start 46: graphmolAdjustQueryCatch 46: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch 46: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 46: Test timeout computed to be: 1500 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 43: [21:31:30] Unusual charge on atom 0 number of radical electrons set to zero 43: [21:31:30] Unusual charge on atom 0 number of radical electrons set to zero 43: [21:31:30] Unusual charge on atom 0 number of radical electrons set to zero 43: [21:31:30] non-ring atom 0 marked aromatic 43: [21:31:30] non-ring atom 0 marked aromatic 43: [21:31:30] Explicit valence for atom # 1 C, 5, is greater than permitted 43: [21:31:30] Explicit valence for atom # 9 C, 5, is greater than permitted 43: [21:31:30] Explicit valence for atom # 3 N, 4, is greater than permitted 43: [21:31:30] Explicit valence for atom # 15 C, 5, is greater than permitted 43: [21:31:30] Explicit valence for atom # 11 C, 5, is greater than permitted 43: [21:31:30] Explicit valence for atom # 9 C, 5, is greater than permitted 43: [21:31:30] Explicit valence for atom # 9 C, 5, is greater than permitted 43: [21:31:30] Explicit valence for atom # 9 C, 6, is greater than permitted 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 7 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 3 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 3 7 43: [21:31:30] Can't kekulize mol. Unkekulized atoms: 3 7 43: [21:31:30] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 43: [21:31:30] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 45: Randomness seeded to: 3513764482 45: =============================================================================== 45: All tests passed (120 assertions in 6 test cases) 45: 36/222 Test #45: graphmolSGroupCatch .................... Passed 0.14 sec test 47 Start 47: chiralityTestsCatch 47: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/chiralityTestsCatch 47: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 47: Test timeout computed to be: 1500 43: [21:31:30] Explicit valence for atom # 1 O, 3, is greater than permitted 43: [21:31:30] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 43: [21:31:30] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 43: [21:31:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 43: [21:31:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 43: =============================================================================== 43: All tests passed (1630 assertions in 89 test cases) 43: 37/222 Test #43: graphmolTestsCatch ..................... Passed 0.33 sec test 48 Start 48: canonTestsCatch 48: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/canonTestsCatch 48: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 48: Test timeout computed to be: 1500 46: Randomness seeded to: 1947290271 46: =============================================================================== 46: All tests passed (281 assertions in 10 test cases) 46: 38/222 Test #46: graphmolAdjustQueryCatch ............... Passed 0.19 sec test 49 Start 49: moliteratorTestsCatch 49: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/moliteratorTestsCatch 49: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 49: Test timeout computed to be: 1500 47: Randomness seeded to: 1033268250 47: [21:31:30] unable to set wavy bonds for double bonds: 3 48: Randomness seeded to: 1677764620 48: =============================================================================== 48: All tests passed (137 assertions in 7 test cases) 48: 39/222 Test #48: canonTestsCatch ........................ Passed 0.06 sec test 50 Start 50: queryTestsCatch 50: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/queryTestsCatch 50: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 50: Test timeout computed to be: 1500 47: [21:31:30] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 47: [21:31:30] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 49: Randomness seeded to: 1309252805 49: =============================================================================== 49: All tests passed (14 assertions in 4 test cases) 49: 40/222 Test #49: moliteratorTestsCatch .................. Passed 0.09 sec test 51 Start 51: molbundleTestsCatch 51: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/molbundleTestsCatch 51: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 51: Test timeout computed to be: 1500 47: [21:31:30] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. 47: [21:31:30] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. 47: [21:31:30] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored 47: [21:31:30] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored 47: [21:31:30] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored 47: =============================================================================== 47: All tests passed (1845 assertions in 63 test cases) 47: 41/222 Test #47: chiralityTestsCatch .................... Passed 0.22 sec test 52 Start 52: pickleTestsCatch 52: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/pickleTestsCatch 52: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 52: Test timeout computed to be: 1500 50: Randomness seeded to: 3158215250 50: =============================================================================== 50: All tests passed (10 assertions in 1 test case) 50: 42/222 Test #50: queryTestsCatch ........................ Passed 0.09 sec test 53 Start 53: smiTest1 53: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 53: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse 53: Test timeout computed to be: 1500 51: Randomness seeded to: 3955922260 51: =============================================================================== 51: All tests passed (6 assertions in 1 test case) 51: 43/222 Test #51: molbundleTestsCatch .................... Passed 0.06 sec test 54 Start 54: smiTest2 54: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 54: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse 54: Test timeout computed to be: 1500 3: dynamic RDAny:0.742136 s 3: static RDValue:1e-06 s 52: Randomness seeded to: 435593753 52: =============================================================================== 52: All tests passed (34 assertions in 1 test case) 52: 44/222 Test #52: pickleTestsCatch ....................... Passed 0.07 sec test 55 Start 55: cxsmilesTest 55: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest 55: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse 55: Test timeout computed to be: 1500 53: [21:31:30] WARNING: not removing hydrogen atom without neighbors 53: [21:31:30] WARNING: not removing hydrogen atom without neighbors 54: [21:31:30] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' 54: [21:31:30] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' 54: [21:31:30] SMILES Parse Error: syntax error while parsing: - 54: [21:31:30] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' 54: [21:31:30] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' 54: [21:31:30] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' 54: [21:31:30] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' 54: [21:31:30] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' 54: [21:31:30] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' 54: [21:31:30] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' 54: [21:31:30] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' 54: [21:31:30] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' 54: [21:31:30] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' 54: [21:31:30] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' 54: [21:31:30] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' 53: [21:31:30] WARNING: not removing hydrogen atom without neighbors 53: [21:31:30] WARNING: not removing hydrogen atom without neighbors 53: [21:31:30] WARNING: not removing hydrogen atom without neighbors 53: [21:31:30] WARNING: not removing hydrogen atom without neighbors 53: [21:31:30] WARNING: not removing hydrogen atom without neighbors 53: [21:31:30] WARNING: not removing hydrogen atom without neighbors 53: [21:31:30] WARNING: not removing hydrogen atom without neighbors 53: [21:31:30] WARNING: not removing hydrogen atom without neighbors 45/222 Test #54: smiTest2 ............................... Passed 0.05 sec test 56 Start 56: smaTest1 56: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 56: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse 56: Test timeout computed to be: 1500 53: [21:31:30] WARNING: not removing hydrogen atom without neighbors 53: [21:31:30] Invalid chiral specification on atom 0 53: [21:31:30] Invalid chiral specification on atom 0 53: [21:31:30] Invalid chiral specification on atom 0 53: [21:31:30] Invalid chiral specification on atom 0 53: [21:31:30] Invalid chiral specification on atom 0 53: [21:31:30] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' 53: [21:31:30] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' 3: dynamic RDValue:0.08518 s 3: deleted! 3: [21:31:30] ------------------------------------- 3: [21:31:30] Testing String Pickle Roundtrips. 3: [21:31:30] done 3: [21:31:30] ------------------------------------- 3: [21:31:30] Testing conversion of vect to string. 3: [21:31:30] done 3: [21:31:30] ------------------------------------- 3: [21:31:30] Testing returning const references. 3: [21:31:30] any cast 3: [21:31:30] done: 0.004387 300000 3: [21:31:30] copy 3: [21:31:30] done: 0.004505 300000 3: [21:31:30] ref 3: [21:31:30] done: 0.004605 300000 3: [21:31:30] dict 3: [21:31:30] done: 0.007557 300000 3: [21:31:30] ref with hasVal 3: [21:31:30] done: 0.005717 300000 3: [21:31:30] done 3: [21:31:30] ------------------------------------- 3: [21:31:30] Testing dict update. 3: [21:31:30] done 3: deleted! 3: deleted! 3: deleted! 3: deleted! 3: deleted! 3: deleted! 46/222 Test #3: testDict ............................... Passed 1.89 sec test 57 Start 57: smiTestCatch 57: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 57: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse 57: Test timeout computed to be: 1500 32: [21:31:30] Maximum BFS search size exceeded. 32: This is likely due to a highly symmetric fused ring system. 53: --C1CCC2(CC1)CCCCC2CCC1CCCC1 53: smi: ClC1CCCCC1 53: smi: ClC1CCCCC1 53: smi: ClC1CCCCC1Br 53: smi: c1ccccc1 53: smi: c1ccncc1 53: smi: c1cc[nH]c1 53: smi: c1cc[nH]c1 53: smi: c1cc[pH]c1 53: CbC(aC)aC 53: CaC(bC)aC 53: CbC(bC)aC 53: O.C 53: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O 53: [21:31:31] SMILES Parse Error: syntax error while parsing: c%()ccccc%() 53: [21:31:31] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' 53: [21:31:31] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) 53: [21:31:31] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' 53: [21:31:31] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' 53: [21:31:31] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' 53: [21:31:31] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 53: [21:31:31] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 53: [21:31:31] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 53: [21:31:31] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 53: [21:31:31] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 53: [21:31:31] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 53: [21:31:31] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 53: [21:31:31] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 53: [21:31:31] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 53: [21:31:31] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 53: [21:31:31] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 53: [21:31:31] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 53: C=c1s/c2n(c1=O)CCCCCCC\N=2 53: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 53: [21:31:31] SMILES Parse Error: extra close parentheses while parsing: C) 53: [21:31:31] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' 47/222 Test #53: smiTest1 ............................... Passed 0.29 sec test 58 Start 58: nontetrahedralCatch 58: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch 58: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse 58: Test timeout computed to be: 1500 58: Randomness seeded to: 2126548519 58: [21:31:31] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 58: [21:31:31] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 58: [21:31:31] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 58: [21:31:31] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 58: [21:31:31] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 58: [21:31:31] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 58: [21:31:31] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 58: [21:31:31] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 58: [21:31:31] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. 58: =============================================================================== 58: All tests passed (308 assertions in 9 test cases) 58: 48/222 Test #58: nontetrahedralCatch .................... Passed 0.12 sec test 59 Start 59: testDepictor 59: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/testDepictor 59: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor 59: Test timeout computed to be: 1500 57: Randomness seeded to: 2542757873 57: [21:31:31] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 57: [21:31:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 57: [21:31:31] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' 57: [21:31:31] SMARTS Parse Error: unclosed ring for input: 'C1C' 57: [21:31:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 57: [21:31:31] SMARTS Parse Error: syntax error while parsing: C)foo 57: [21:31:31] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' 57: [21:31:31] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| 57: [21:31:31] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' 57: [21:31:31] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' 56: [21:31:31] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC 56: [21:31:31] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' 56: [21:31:31] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON 56: [21:31:31] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' 59: 59: RDKit 2D 59: 59: 8 9 0 0 0 0 0 0 0 0999 V2000 59: 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 59: 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 59: -0.7500 -1.2990 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 59: -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 59: -0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 59: 0.7500 1.2990 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 59: 0.2954 0.6125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 59: -0.3828 -0.5621 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 59: 1 2 1 0 59: 2 3 1 0 59: 3 4 1 0 59: 4 5 1 0 59: 5 6 1 0 59: 6 7 1 0 59: 7 8 1 0 59: 6 1 1 0 59: 8 3 1 0 59: M END 59: 59: 59: RDKit 2D 59: 59: 8 9 0 0 0 0 0 0 0 0999 V2000 59: 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 59: 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 59: -0.7500 -1.2990 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 59: -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 59: -0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 59: 0.7500 1.2990 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 59: -0.4000 0.6928 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 59: -0.8000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 59: 1 2 1 0 59: 2 3 1 0 59: 3 4 1 0 59: 4 5 1 0 59: 5 6 1 0 59: 6 7 1 0 59: 7 8 1 0 59: 6 1 1 0 59: 8 3 1 0 59: M END 59: 56: [21:31:31] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 56: [21:31:31] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 49/222 Test #56: smaTest1 ............................... Passed 0.64 sec test 60 Start 60: depictorCatch 60: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/depictorCatch 60: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor 60: Test timeout computed to be: 1500 57: [21:31:31] w block attempts to set wedging on bond 0 more than once. 57: [21:31:31] improperly formatted w block 57: [21:31:31] atom 3 is not associated with bond 1 in w block 57: =============================================================================== 57: All tests passed (1516 assertions in 53 test cases) 57: 50/222 Test #57: smiTestCatch ........................... Passed 0.75 sec test 61 Start 61: pyDepictor 61: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap/testDepictor.py" 61: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap 61: Test timeout computed to be: 1500 32: [21:31:31] Maximum BFS search size exceeded. 32: This is likely due to a highly symmetric fused ring system. 32: F/C=C/Cl 32: [H]/C(F)=C(/[H])Cl 32: F/C=C/Cl 32: F/C=C/Cl 32: C/C(F)=C(/C)Cl 51/222 Test #32: graphmolMolOpsTest ..................... Passed 1.97 sec test 62 Start 62: testMrvToMol 62: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 62: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MarvinParse 62: Test timeout computed to be: 1500 59: [21:31:32] Warning: stereochemistry around double bond may be incorrect in depiction. 60: Randomness seeded to: 1598616874 60: =============================================================================== 60: All tests passed (571 assertions in 14 test cases) 60: 52/222 Test #60: depictorCatch .......................... Passed 0.64 sec test 63 Start 63: fileParsersTest1 63: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 63: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 63: Test timeout computed to be: 1500 53/222 Test #59: testDepictor ........................... Passed 1.02 sec test 64 Start 64: testMolSupplier 64: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 64: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 64: Test timeout computed to be: 1500 55: Randomness seeded to: 349519989 55: =============================================================================== 55: All tests passed (1902 assertions in 21 test cases) 55: 54/222 Test #55: cxsmilesTest ........................... Passed 1.46 sec test 65 Start 65: testGeneralFileReader 65: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader 65: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 65: Test timeout computed to be: 1500 64: [21:31:32] 64: ----------------------------------------- 62: Using new chirality perception 62: Test 62: 62: NewChiralTest.sdf 62: 62: Test 62: 62: NewChiralTest.sdf 62: 62: Test 62: 62: NewChiralTestNoChiral.sdf 62: 62: Test 62: 62: NewChiralTestNoChiral.sdf 62: 62: Test 62: 62: NewChiralTestAllChiral.sdf 62: 62: Test 62: 62: NewChiralTestAllChiral.sdf 62: 62: Test 62: 62: ProblemShort.mol 62: 62: [21:31:32] For a MultipleSgroup expansion, the matching orphaned bond was not found 62: The multiple sgroup will be ignored 65: [21:31:32] 65: ----------------------------------------- 65: [21:31:32] Finished: testDetermineFormat() 65: [21:31:32] ----------------------------------------- 65: 65: [21:31:32] 65: ----------------------------------------- 63: *************************************** 63: *************************************** 63: [21:31:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: [21:31:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 64: [21:31:32] 64: 64: **** 64: Invariant Violation 64: bad prop value 64: Violation occurred on line 158 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 64: Failed Expression: nSwaps < 2 64: **** 64: 65: [21:31:32] Finished: testSdf() 65: [21:31:32] ----------------------------------------- 65: 65: [21:31:32] 65: ----------------------------------------- 55/222 Test #61: pyDepictor .............................***Exception: SegFault 0.79 sec test 66 Start 66: testMultithreadedMolSupplier 66: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier 66: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 66: Test timeout computed to be: 1500 65: [21:31:32] Finished: testSmi() 65: [21:31:32] ----------------------------------------- 65: 65: [21:31:32] 65: ----------------------------------------- 66: [21:31:32] 66: ----------------------------------------- 63: [21:31:32] bond with order 0 found on line 7. This is not part of the MDL specification. 64: [21:31:32] Finished: testMolSup() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testRandMolSup() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 65: [21:31:32] Finished: testMae() 65: [21:31:32] ----------------------------------------- 65: 65: [21:31:32] 65: ----------------------------------------- 65: [21:31:32] Finished: testTdt() 65: [21:31:32] ----------------------------------------- 65: 56/222 Test #65: testGeneralFileReader .................. Passed 0.40 sec test 67 Start 67: testMolWriter 67: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolWriter 67: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 67: Test timeout computed to be: 1500 64: [21:31:32] Finished: testSmilesSup() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] ------------------------------------------------------ 64: [21:31:32] SMILES Parse Error: syntax error while parsing: fail 64: [21:31:32] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' 64: [21:31:32] ERROR: Smiles parse error on line 3 64: [21:31:32] ERROR: Cannot create molecule from : 'fail' 64: [21:31:32] ------------------------------------------------------ 64: [21:31:32] ------------------------------------------------------ 64: [21:31:32] >>> This may result in an infinite loop. It should finish almost immediately: 64: [21:31:32] <<< done. 64: [21:31:32] Finished: testSmilesSupFromText() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testSmilesWriter() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 63: [21:31:32] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) 63: [21:31:32] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) 63: [21:31:32] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 64: [21:31:32] Finished: testSDWriter() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testSDSupplierEnding() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testSuppliersEmptyFile() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testCisTrans() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testStereoRound() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 64: [21:31:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 64: [21:31:32] Finished: testIssue226() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testTDTSupplier1() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testTDTSupplier2() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testTDTSupplier3() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testSDSupplierFromText() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 63: generating smiles 63: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 63: converting back 64: [21:31:32] ERROR: Problems encountered parsing data fields 64: [21:31:32] ERROR: moving to the beginning of the next molecule 64: [21:31:32] ERROR: Problems encountered parsing data fields 64: [21:31:32] ERROR: moving to the beginning of the next molecule 64: [21:31:32] Spurious data before the first property will be ignored 64: [21:31:32] Property will be truncated after the first blank line 64: [21:31:32] Property will be truncated after the first blank line 64: [21:31:32] Property will be truncated after the first blank line 64: [21:31:32] Finished: testSDSupplierStrLax1() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] ERROR: Problems encountered parsing data fields 64: [21:31:32] ERROR: moving to the beginning of the next molecule 64: [21:31:32] Property will be truncated after the first blank line 64: [21:31:32] Finished: testSDSupplierStrLax2() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] ERROR: Problems encountered parsing data fields 64: [21:31:32] ERROR: moving to the beginning of the next molecule 64: [21:31:32] ERROR: Problems encountered parsing data fields 64: [21:31:32] ERROR: moving to the beginning of the next molecule 64: [21:31:32] Spurious data before the first property will be ignored 64: [21:31:32] Property will be truncated after the first blank line 64: [21:31:32] Property will be truncated after the first blank line 64: [21:31:32] Property will be truncated after the first blank line 64: [21:31:32] Finished: testSDSupplierFromTextStrLax1() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] ERROR: Problems encountered parsing data fields 64: [21:31:32] ERROR: moving to the beginning of the next molecule 64: [21:31:32] Property will be truncated after the first blank line 64: [21:31:32] Finished: testSDSupplierFromTextStrLax2() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testIssue265() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] ERROR: End of data field name not found 64: [21:31:32] ERROR: moving to the beginning of the next molecule 64: [21:31:32] Explicit valence for atom # 0 F, 2, is greater than permitted 64: [21:31:32] ERROR: Could not sanitize molecule ending on line 16 64: [21:31:32] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted 63: check isomorphism 64: [21:31:32] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 64: [21:31:32] ERROR: moving to the beginning of the next molecule 64: [21:31:32] ERROR: Bond line too short: 'M END' on line 18 64: [21:31:32] ERROR: moving to the beginning of the next molecule 64: [21:31:32] Finished: testSDErrorHandling() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testIssue381() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testSetStreamIndices() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testMixIterAndRandom() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: build: 64: [21:31:32] Finished: testRemoveHs() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testGetItemText() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testForwardSDSupplier() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testMissingCRSDSupplier() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testIssue3482695() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] ERROR: Cannot convert 'foo' to unsigned int on line 557 64: [21:31:32] ERROR: moving to the beginning of the next molecule 64: [21:31:32] Finished: testIssue3525673() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testBlankLinesInProps() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testSkipLines() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testGitHub23() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testGitHub88() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testGitHub2285() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 64: [21:31:32] ERROR: Smiles parse error on line 1 64: [21:31:32] ERROR: Cannot create molecule from : 'c1ccccc' 64: [21:31:32] SMILES Parse Error: extra open parentheses for input: 'C(C' 64: [21:31:32] ERROR: Smiles parse error on line 3 64: [21:31:32] ERROR: Cannot create molecule from : 'C(C' 64: [21:31:32] Explicit valence for atom # 1 C, 5, is greater than permitted 64: [21:31:32] ERROR: Could not sanitize molecule on line 5 64: [21:31:32] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted 64: [21:31:32] Explicit valence for atom # 1 F, 2, is greater than permitted 64: [21:31:32] ERROR: Could not sanitize molecule ending on line 21 64: [21:31:32] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 64: [21:31:32] Explicit valence for atom # 1 F, 2, is greater than permitted 64: [21:31:32] ERROR: Could not sanitize molecule ending on line 21 64: [21:31:32] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 64: [21:31:32] Explicit valence for atom # 1 F, 2, is greater than permitted 64: [21:31:32] ERROR: Could not sanitize molecule ending on line 21 64: [21:31:32] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 64: [21:31:32] ERROR: Atom line too short: ' -9.6' on line 28 64: [21:31:32] ERROR: moving to the beginning of the next molecule 64: [21:31:32] Explicit valence for atom # 1 F, 2, is greater than permitted 64: [21:31:32] ERROR: Could not sanitize molecule ending on line 21 64: [21:31:32] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 64: [21:31:32] ERROR: Atom line too short: ' -9.6' on line 28 64: [21:31:32] ERROR: moving to the beginning of the next molecule 64: [21:31:32] Finished: testGitHub2479() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] 64: 64: **** 64: Invariant Violation 64: bad chiral bond 64: Violation occurred on line 164 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 64: Failed Expression: bnd 64: **** 64: 64: [21:31:32] Finished: testGitHub2881() 64: [21:31:32] ----------------------------------------- 64: 64: [21:31:32] ----------------------------------------- 64: [21:31:32] Finished: testGitHub3517() 64: [21:31:32] ----------------------------------------- 64: 57/222 Test #64: testMolSupplier ........................ Passed 0.76 sec test 68 Start 68: testTplParser 68: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testTplParser 68: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 68: Test timeout computed to be: 1500 58/222 Test #68: testTplParser .......................... Passed 0.11 sec test 69 Start 69: testMol2ToMol 69: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol 69: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 69: Test timeout computed to be: 1500 59/222 Test #69: testMol2ToMol .......................... Passed 0.22 sec test 70 Start 70: testSequence 70: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testSequence 70: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 70: Test timeout computed to be: 1500 67: [21:31:33] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 67: [21:31:33] bond with order 0 found on line 11. This is not part of the MDL specification. 67: [21:31:33] bond with order 0 found on line 16. This is not part of the MDL specification. 70: Sequence: GREG 70: HELM: PEPTIDE1{G.R.E.G}$$$$ 70: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O 70: PDB: 70: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 70: CONECT 1 2 70: CONECT 2 3 70: CONECT 3 4 4 5 70: CONECT 5 6 70: CONECT 6 7 9 70: CONECT 7 8 8 16 70: CONECT 9 10 70: CONECT 10 11 70: CONECT 11 12 70: CONECT 12 13 70: CONECT 13 14 14 15 70: CONECT 16 17 70: CONECT 17 18 20 70: CONECT 18 19 19 25 70: CONECT 20 21 70: CONECT 21 22 70: CONECT 22 23 23 24 70: CONECT 25 26 70: CONECT 26 27 70: CONECT 27 28 28 29 70: END 70: 70: Sequence: TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN 70: HELM: PEPTIDE1{T.T.C.C.P.S.I.V.A.R.S.N.F.N.V.C.R.L.P.G.T.P.E.A.I.C.A.T.Y.T.G.C.I.I.I.P.G.A.T.C.P.G.D.Y.A.N}$$$$ 70: Smiles: CC[C@H](C)[C@H](NC(=O)[C@H](C)NC(=O)[C@H](CCC(=O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H](NC(=O)CNC(=O)[C@@H]1CCCN1C(=O)[C@H](CC(C)C)NC(=O)[C@H](CCCNC(=N)N)NC(=O)[C@H](CS)NC(=O)[C@@H](NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CO)NC(=O)[C@H](CCCNC(=N)N)NC(=O)[C@H](C)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](CO)NC(=O)[C@@H]1CCCN1C(=O)[C@H](CS)NC(=O)[C@H](CS)NC(=O)[C@@H](NC(=O)[C@@H](N)[C@@H](C)O)[C@@H](C)O)[C@@H](C)CC)C(C)C)C(C)C)[C@@H](C)O)C(=O)N[C@@H](CS)C(=O)N[C@@H](C)C(=O)N[C@H](C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@H](C(=O)NCC(=O)N[C@@H](CS)C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N1CCC[C@H]1C(=O)NCC(=O)N[C@@H](C)C(=O)N[C@H](C(=O)N[C@@H](CS)C(=O)N1CCC[C@H]1C(=O)NCC(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H](C)C(=O)N[C@@H](CC(N)=O)C(=O)O)[C@@H](C)O)[C@@H](C)CC)[C@@H](C)CC)[C@@H](C)CC)[C@@H](C)O)[C@@H](C)O 70: PDB: 70: ATOM 1 N THR A 1 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 2 CA THR A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 3 C THR A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 4 O THR A 1 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 5 CB THR A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 6 OG1 THR A 1 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 7 CG2 THR A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 8 N THR A 2 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 9 CA THR A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 10 C THR A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 11 O THR A 2 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 12 CB THR A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 13 OG1 THR A 2 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 14 CG2 THR A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 15 N CYS A 3 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 16 CA CYS A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 17 C CYS A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 18 O CYS A 3 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 19 CB CYS A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 20 SG CYS A 3 0.000 0.000 0.000 1.00 0.00 S 70: ATOM 21 N CYS A 4 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 22 CA CYS A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 23 C CYS A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 24 O CYS A 4 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 25 CB CYS A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 26 SG CYS A 4 0.000 0.000 0.000 1.00 0.00 S 70: ATOM 27 N PRO A 5 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 28 CA PRO A 5 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 29 C PRO A 5 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 30 O PRO A 5 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 31 CB PRO A 5 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 32 CG PRO A 5 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 33 CD PRO A 5 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 34 N SER A 6 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 35 CA SER A 6 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 36 C SER A 6 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 37 O SER A 6 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 38 CB SER A 6 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 39 OG SER A 6 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 40 N ILE A 7 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 41 CA ILE A 7 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 42 C ILE A 7 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 43 O ILE A 7 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 44 CB ILE A 7 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 45 CG1 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 46 CG2 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 47 CD1 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 48 N VAL A 8 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 49 CA VAL A 8 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 50 C VAL A 8 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 51 O VAL A 8 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 52 CB VAL A 8 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 53 CG1 VAL A 8 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 54 CG2 VAL A 8 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 55 N ALA A 9 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 56 CA ALA A 9 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 57 C ALA A 9 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 58 O ALA A 9 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 59 CB ALA A 9 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 60 N ARG A 10 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 61 CA ARG A 10 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 62 C ARG A 10 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 63 O ARG A 10 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 64 CB ARG A 10 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 65 CG ARG A 10 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 66 CD ARG A 10 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 67 NE ARG A 10 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 68 CZ ARG A 10 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 69 NH1 ARG A 10 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 70 NH2 ARG A 10 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 71 N SER A 11 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 72 CA SER A 11 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 73 C SER A 11 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 74 O SER A 11 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 75 CB SER A 11 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 76 OG SER A 11 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 77 N ASN A 12 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 78 CA ASN A 12 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 79 C ASN A 12 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 80 O ASN A 12 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 81 CB ASN A 12 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 82 CG ASN A 12 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 83 OD1 ASN A 12 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 84 ND2 ASN A 12 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 85 N PHE A 13 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 86 CA PHE A 13 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 87 C PHE A 13 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 88 O PHE A 13 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 89 CB PHE A 13 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 90 CG PHE A 13 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 91 CD1 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 92 CD2 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 93 CE1 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 94 CE2 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 95 CZ PHE A 13 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 96 N ASN A 14 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 97 CA ASN A 14 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 98 C ASN A 14 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 99 O ASN A 14 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 100 CB ASN A 14 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 101 CG ASN A 14 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 102 OD1 ASN A 14 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 103 ND2 ASN A 14 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 104 N VAL A 15 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 105 CA VAL A 15 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 106 C VAL A 15 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 107 O VAL A 15 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 108 CB VAL A 15 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 109 CG1 VAL A 15 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 110 CG2 VAL A 15 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 111 N CYS A 16 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 112 CA CYS A 16 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 113 C CYS A 16 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 114 O CYS A 16 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 115 CB CYS A 16 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 116 SG CYS A 16 0.000 0.000 0.000 1.00 0.00 S 70: ATOM 117 N ARG A 17 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 118 CA ARG A 17 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 119 C ARG A 17 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 120 O ARG A 17 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 121 CB ARG A 17 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 122 CG ARG A 17 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 123 CD ARG A 17 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 124 NE ARG A 17 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 125 CZ ARG A 17 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 126 NH1 ARG A 17 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 127 NH2 ARG A 17 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 128 N LEU A 18 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 129 CA LEU A 18 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 130 C LEU A 18 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 131 O LEU A 18 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 132 CB LEU A 18 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 133 CG LEU A 18 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 134 CD1 LEU A 18 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 135 CD2 LEU A 18 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 136 N PRO A 19 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 137 CA PRO A 19 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 138 C PRO A 19 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 139 O PRO A 19 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 140 CB PRO A 19 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 141 CG PRO A 19 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 142 CD PRO A 19 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 143 N GLY A 20 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 144 CA GLY A 20 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 145 C GLY A 20 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 146 O GLY A 20 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 147 N THR A 21 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 148 CA THR A 21 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 149 C THR A 21 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 150 O THR A 21 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 151 CB THR A 21 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 152 OG1 THR A 21 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 153 CG2 THR A 21 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 154 N PRO A 22 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 155 CA PRO A 22 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 156 C PRO A 22 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 157 O PRO A 22 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 158 CB PRO A 22 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 159 CG PRO A 22 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 160 CD PRO A 22 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 161 N GLU A 23 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 162 CA GLU A 23 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 163 C GLU A 23 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 164 O GLU A 23 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 165 CB GLU A 23 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 166 CG GLU A 23 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 167 CD GLU A 23 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 168 OE1 GLU A 23 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 169 OE2 GLU A 23 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 170 N ALA A 24 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 171 CA ALA A 24 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 172 C ALA A 24 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 173 O ALA A 24 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 174 CB ALA A 24 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 175 N ILE A 25 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 176 CA ILE A 25 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 177 C ILE A 25 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 178 O ILE A 25 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 179 CB ILE A 25 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 180 CG1 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 181 CG2 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 182 CD1 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 183 N CYS A 26 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 184 CA CYS A 26 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 185 C CYS A 26 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 186 O CYS A 26 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 187 CB CYS A 26 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 188 SG CYS A 26 0.000 0.000 0.000 1.00 0.00 S 70: ATOM 189 N ALA A 27 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 190 CA ALA A 27 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 191 C ALA A 27 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 192 O ALA A 27 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 193 CB ALA A 27 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 194 N THR A 28 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 195 CA THR A 28 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 196 C THR A 28 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 197 O THR A 28 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 198 CB THR A 28 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 199 OG1 THR A 28 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 200 CG2 THR A 28 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 201 N TYR A 29 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 202 CA TYR A 29 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 203 C TYR A 29 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 204 O TYR A 29 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 205 CB TYR A 29 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 206 CG TYR A 29 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 207 CD1 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 208 CD2 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 209 CE1 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 210 CE2 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 211 CZ TYR A 29 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 212 OH TYR A 29 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 213 N THR A 30 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 214 CA THR A 30 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 215 C THR A 30 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 216 O THR A 30 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 217 CB THR A 30 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 218 OG1 THR A 30 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 219 CG2 THR A 30 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 220 N GLY A 31 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 221 CA GLY A 31 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 222 C GLY A 31 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 223 O GLY A 31 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 224 N CYS A 32 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 225 CA CYS A 32 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 226 C CYS A 32 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 227 O CYS A 32 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 228 CB CYS A 32 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 229 SG CYS A 32 0.000 0.000 0.000 1.00 0.00 S 70: ATOM 230 N ILE A 33 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 231 CA ILE A 33 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 232 C ILE A 33 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 233 O ILE A 33 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 234 CB ILE A 33 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 235 CG1 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 236 CG2 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 237 CD1 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 238 N ILE A 34 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 239 CA ILE A 34 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 240 C ILE A 34 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 241 O ILE A 34 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 242 CB ILE A 34 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 243 CG1 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 244 CG2 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 245 CD1 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 246 N ILE A 35 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 247 CA ILE A 35 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 248 C ILE A 35 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 249 O ILE A 35 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 250 CB ILE A 35 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 251 CG1 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 252 CG2 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 253 CD1 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 254 N PRO A 36 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 255 CA PRO A 36 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 256 C PRO A 36 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 257 O PRO A 36 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 258 CB PRO A 36 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 259 CG PRO A 36 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 260 CD PRO A 36 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 261 N GLY A 37 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 262 CA GLY A 37 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 263 C GLY A 37 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 264 O GLY A 37 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 265 N ALA A 38 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 266 CA ALA A 38 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 267 C ALA A 38 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 268 O ALA A 38 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 269 CB ALA A 38 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 270 N THR A 39 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 271 CA THR A 39 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 272 C THR A 39 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 273 O THR A 39 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 274 CB THR A 39 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 275 OG1 THR A 39 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 276 CG2 THR A 39 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 277 N CYS A 40 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 278 CA CYS A 40 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 279 C CYS A 40 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 280 O CYS A 40 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 281 CB CYS A 40 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 282 SG CYS A 40 0.000 0.000 0.000 1.00 0.00 S 70: ATOM 283 N PRO A 41 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 284 CA PRO A 41 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 285 C PRO A 41 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 286 O PRO A 41 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 287 CB PRO A 41 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 288 CG PRO A 41 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 289 CD PRO A 41 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 290 N GLY A 42 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 291 CA GLY A 42 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 292 C GLY A 42 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 293 O GLY A 42 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 294 N ASP A 43 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 295 CA ASP A 43 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 296 C ASP A 43 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 297 O ASP A 43 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 298 CB ASP A 43 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 299 CG ASP A 43 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 300 OD1 ASP A 43 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 301 OD2 ASP A 43 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 302 N TYR A 44 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 303 CA TYR A 44 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 304 C TYR A 44 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 305 O TYR A 44 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 306 CB TYR A 44 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 307 CG TYR A 44 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 308 CD1 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 309 CD2 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 310 CE1 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 311 CE2 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 312 CZ TYR A 44 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 313 OH TYR A 44 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 314 N ALA A 45 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 315 CA ALA A 45 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 316 C ALA A 45 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 317 O ALA A 45 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 318 CB ALA A 45 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 319 N ASN A 46 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 320 CA ASN A 46 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 321 C ASN A 46 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 322 O ASN A 46 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 323 CB ASN A 46 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 324 CG ASN A 46 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 325 OD1 ASN A 46 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 326 ND2 ASN A 46 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 327 OXT ASN A 46 0.000 0.000 0.000 1.00 0.00 O 70: CONECT 1 2 70: CONECT 2 3 5 70: CONECT 3 4 4 8 70: CONECT 5 6 7 70: CONECT 8 9 70: CONECT 9 10 12 70: CONECT 10 11 11 15 70: CONECT 12 13 14 70: CONECT 15 16 70: CONECT 16 17 19 70: CONECT 17 18 18 21 70: CONECT 19 20 70: CONECT 21 22 70: CONECT 22 23 25 70: CONECT 23 24 24 27 70: CONECT 25 26 70: CONECT 27 28 33 70: CONECT 28 29 31 70: CONECT 29 30 30 34 70: CONECT 31 32 70: CONECT 32 33 70: CONECT 34 35 70: CONECT 35 36 38 70: CONECT 36 37 37 40 70: CONECT 38 39 70: CONECT 40 41 70: CONECT 41 42 44 70: CONECT 42 43 43 48 70: CONECT 44 45 46 70: CONECT 46 47 70: CONECT 48 49 70: CONECT 49 50 52 70: CONECT 50 51 51 55 70: CONECT 52 53 54 70: CONECT 55 56 70: CONECT 56 57 59 70: CONECT 57 58 58 60 70: CONECT 60 61 70: CONECT 61 62 64 70: CONECT 62 63 63 71 70: CONECT 64 65 70: CONECT 65 66 70: CONECT 66 67 70: CONECT 67 68 70: CONECT 68 69 69 70 70: CONECT 71 72 70: CONECT 72 73 75 70: CONECT 73 74 74 77 70: CONECT 75 76 70: CONECT 77 78 70: CONECT 78 79 81 70: CONECT 79 80 80 85 70: CONECT 81 82 70: CONECT 82 83 83 84 70: CONECT 85 86 70: CONECT 86 87 89 70: CONECT 87 88 88 96 70: CONECT 89 90 70: CONECT 90 91 91 92 70: CONECT 91 93 70: CONECT 92 94 94 70: CONECT 93 95 95 70: CONECT 94 95 70: CONECT 96 97 70: CONECT 97 98 100 70: CONECT 98 99 99 104 70: CONECT 100 101 70: CONECT 101 102 102 103 70: CONECT 104 105 70: CONECT 105 106 108 70: CONECT 106 107 107 111 70: CONECT 108 109 110 70: CONECT 111 112 70: CONECT 112 113 115 70: CONECT 113 114 114 117 70: CONECT 115 116 70: CONECT 117 118 70: CONECT 118 119 121 70: CONECT 119 120 120 128 70: CONECT 121 122 70: CONECT 122 123 70: CONECT 123 124 70: CONECT 124 125 70: CONECT 125 126 126 127 70: CONECT 128 129 70: CONECT 129 130 132 70: CONECT 130 131 131 136 70: CONECT 132 133 70: CONECT 133 134 135 70: CONECT 136 137 142 70: CONECT 137 138 140 70: CONECT 138 139 139 143 70: CONECT 140 141 70: CONECT 141 142 70: CONECT 143 144 70: CONECT 144 145 70: CONECT 145 146 146 147 70: CONECT 147 148 70: CONECT 148 149 151 70: CONECT 149 150 150 154 70: CONECT 151 152 153 70: CONECT 154 155 160 70: CONECT 155 156 158 70: CONECT 156 157 157 161 70: CONECT 158 159 70: CONECT 159 160 70: CONECT 161 162 70: CONECT 162 163 165 70: CONECT 163 164 164 170 70: CONECT 165 166 70: CONECT 166 167 70: CONECT 167 168 168 169 70: CONECT 170 171 70: CONECT 171 172 174 70: CONECT 172 173 173 175 70: CONECT 175 176 70: CONECT 176 177 179 70: CONECT 177 178 178 183 70: CONECT 179 180 181 70: CONECT 181 182 70: CONECT 183 184 70: CONECT 184 185 187 70: CONECT 185 186 186 189 70: CONECT 187 188 70: CONECT 189 190 70: CONECT 190 191 193 70: CONECT 191 192 192 194 70: CONECT 194 195 70: CONECT 195 196 198 70: CONECT 196 197 197 201 70: CONECT 198 199 200 70: CONECT 201 202 70: CONECT 202 203 205 70: CONECT 203 204 204 213 70: CONECT 205 206 70: CONECT 206 207 207 208 70: CONECT 207 209 70: CONECT 208 210 210 70: CONECT 209 211 211 70: CONECT 210 211 70: CONECT 211 212 70: CONECT 213 214 70: CONECT 214 215 217 70: CONECT 215 216 216 220 70: CONECT 217 218 219 70: CONECT 220 221 70: CONECT 221 222 70: CONECT 222 223 223 224 70: CONECT 224 225 70: CONECT 225 226 228 70: CONECT 226 227 227 230 70: CONECT 228 229 70: CONECT 230 231 70: CONECT 231 232 234 70: CONECT 232 233 233 238 70: CONECT 234 235 236 70: CONECT 236 237 70: CONECT 238 239 70: CONECT 239 240 242 70: CONECT 240 241 241 246 70: CONECT 242 243 244 70: CONECT 244 245 70: CONECT 246 247 70: CONECT 247 248 250 70: CONECT 248 249 249 254 70: CONECT 250 251 252 70: CONECT 252 253 70: CONECT 254 255 260 70: CONECT 255 256 258 70: CONECT 256 257 257 261 70: CONECT 258 259 70: CONECT 259 260 70: CONECT 261 262 70: CONECT 262 263 70: CONECT 263 264 264 265 70: CONECT 265 266 70: CONECT 266 267 269 70: CONECT 267 268 268 270 70: CONECT 270 271 70: CONECT 271 272 274 70: CONECT 272 273 273 277 70: CONECT 274 275 276 70: CONECT 277 278 70: CONECT 278 279 281 70: CONECT 279 280 280 283 70: CONECT 281 282 70: CONECT 283 284 289 70: CONECT 284 285 287 70: CONECT 285 286 286 290 70: CONECT 287 288 70: CONECT 288 289 70: CONECT 290 291 70: CONECT 291 292 70: CONECT 292 293 293 294 70: CONECT 294 295 70: CONECT 295 296 298 70: CONECT 296 297 297 302 70: CONECT 298 299 70: CONECT 299 300 300 301 70: CONECT 302 303 70: CONECT 303 304 306 70: CONECT 304 305 305 314 70: CONECT 306 307 70: CONECT 307 308 308 309 70: CONECT 308 310 70: CONECT 309 311 311 70: CONECT 310 312 312 70: CONECT 311 312 70: CONECT 312 313 70: CONECT 314 315 70: CONECT 315 316 318 70: CONECT 316 317 317 319 70: CONECT 319 320 70: CONECT 320 321 323 70: CONECT 321 322 322 327 70: CONECT 323 324 70: CONECT 324 325 325 326 70: END 70: 70: Sequence: GREG 70: HELM: PEPTIDE1{G.R.E.G}$$$$ 70: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O 70: PDB: 70: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 70: CONECT 1 2 70: CONECT 2 3 70: CONECT 3 4 4 5 70: CONECT 5 6 70: CONECT 6 7 9 70: CONECT 7 8 8 16 70: CONECT 9 10 70: CONECT 10 11 70: CONECT 11 12 70: CONECT 12 13 70: CONECT 13 14 14 15 70: CONECT 16 17 70: CONECT 17 18 20 70: CONECT 18 19 19 25 70: CONECT 20 21 70: CONECT 21 22 70: CONECT 22 23 23 24 70: CONECT 25 26 70: CONECT 26 27 70: CONECT 27 28 28 29 70: END 70: 70: Sequence: CYIQNCPLG 70: HELM: PEPTIDE1{C.Y.I.Q.N.C.P.L.G.[am]}$PEPTIDE1,PEPTIDE1,1:R3-6:R3$$$ 70: Smiles: CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccc(O)cc2)NC(=O)[C@@H](N)CSSC[C@@H](C(=O)N2CCC[C@H]2C(=O)N[C@@H](CC(C)C)C(=O)NCC(N)=O)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CCC(N)=O)NC1=O 70: PDB: 70: ATOM 1 N CYS A 1 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 2 CA CYS A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 3 C CYS A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 4 O CYS A 1 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 5 CB CYS A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 6 SG CYS A 1 0.000 0.000 0.000 1.00 0.00 S 70: ATOM 7 N TYR A 2 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 8 CA TYR A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 9 C TYR A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 10 O TYR A 2 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 11 CB TYR A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 12 CG TYR A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 13 CD1 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 14 CD2 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 15 CE1 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 16 CE2 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 17 CZ TYR A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 18 OH TYR A 2 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 19 N ILE A 3 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 20 CA ILE A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 21 C ILE A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 22 O ILE A 3 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 23 CB ILE A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 24 CG1 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 25 CG2 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 26 CD1 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 27 N GLN A 4 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 28 CA GLN A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 29 C GLN A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 30 O GLN A 4 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 31 CB GLN A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 32 CG GLN A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 33 CD GLN A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 34 OE1 GLN A 4 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 35 NE2 GLN A 4 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 36 N ASN A 5 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 37 CA ASN A 5 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 38 C ASN A 5 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 39 O ASN A 5 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 40 CB ASN A 5 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 41 CG ASN A 5 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 42 OD1 ASN A 5 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 43 ND2 ASN A 5 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 44 N CYS A 6 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 45 CA CYS A 6 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 46 C CYS A 6 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 47 O CYS A 6 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 48 CB CYS A 6 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 49 SG CYS A 6 0.000 0.000 0.000 1.00 0.00 S 70: ATOM 50 N PRO A 7 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 51 CA PRO A 7 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 52 C PRO A 7 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 53 O PRO A 7 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 54 CB PRO A 7 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 55 CG PRO A 7 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 56 CD PRO A 7 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 57 N LEU A 8 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 58 CA LEU A 8 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 59 C LEU A 8 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 60 O LEU A 8 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 61 CB LEU A 8 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 62 CG LEU A 8 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 63 CD1 LEU A 8 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 64 CD2 LEU A 8 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 65 N GLY A 9 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 66 CA GLY A 9 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 67 C GLY A 9 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 68 O GLY A 9 0.000 0.000 0.000 1.00 0.00 O 70: HETATM 69 N NH2 A 10 0.000 0.000 0.000 1.00 0.00 N 70: CONECT 1 2 70: CONECT 2 3 5 70: CONECT 3 4 4 7 70: CONECT 5 6 70: CONECT 6 49 70: CONECT 7 8 70: CONECT 8 9 11 70: CONECT 9 10 10 19 70: CONECT 11 12 70: CONECT 12 13 13 14 70: CONECT 13 15 70: CONECT 14 16 16 70: CONECT 15 17 17 70: CONECT 16 17 70: CONECT 17 18 70: CONECT 19 20 70: CONECT 20 21 23 70: CONECT 21 22 22 27 70: CONECT 23 24 25 70: CONECT 25 26 70: CONECT 27 28 70: CONECT 28 29 31 70: CONECT 29 30 30 36 70: CONECT 31 32 70: CONECT 32 33 70: CONECT 33 34 34 35 70: CONECT 36 37 70: CONECT 37 38 40 70: CONECT 38 39 39 44 70: CONECT 40 41 70: CONECT 41 42 42 43 70: CONECT 44 45 70: CONECT 45 46 48 70: CONECT 46 47 47 50 70: CONECT 48 49 70: CONECT 50 51 56 70: CONECT 51 52 54 70: CONECT 52 53 53 57 70: CONECT 54 55 70: CONECT 55 56 70: CONECT 57 58 70: CONECT 58 59 61 70: CONECT 59 60 60 65 70: CONECT 61 62 70: CONECT 62 63 64 70: CONECT 65 66 70: CONECT 66 67 70: CONECT 67 68 68 69 70: END 70: 70: Sequence: LfPVXLfPVX 70: HELM: PEPTIDE1{L.[dF].P.V.[Orn].L.[dF].P.V.[Orn]}$PEPTIDE1,PEPTIDE1,10:R2-1:R1$$$ 70: Smiles: CC(C)C[C@@H]1NC(=O)[C@H](CCCN)NC(=O)[C@H](C(C)C)NC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CCCN)NC(=O)[C@H](C(C)C)NC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc2ccccc2)NC1=O 70: PDB: 70: ATOM 1 N LEU A 1 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 2 CA LEU A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 3 C LEU A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 4 O LEU A 1 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 5 CB LEU A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 6 CG LEU A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 7 CD1 LEU A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 8 CD2 LEU A 1 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 9 N DPN A 2 0.000 0.000 0.000 1.00 0.00 N 70: HETATM 10 CA DPN A 2 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 11 C DPN A 2 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 12 O DPN A 2 0.000 0.000 0.000 1.00 0.00 O 70: HETATM 13 CB DPN A 2 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 14 CG DPN A 2 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 15 CD1 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 16 CD2 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 17 CE1 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 18 CE2 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 19 CZ DPN A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 20 N PRO A 3 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 21 CA PRO A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 22 C PRO A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 23 O PRO A 3 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 24 CB PRO A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 25 CG PRO A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 26 CD PRO A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 27 N VAL A 4 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 28 CA VAL A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 29 C VAL A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 30 O VAL A 4 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 31 CB VAL A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 32 CG1 VAL A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 33 CG2 VAL A 4 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 34 N ORN A 5 0.000 0.000 0.000 1.00 0.00 N 70: HETATM 35 CA ORN A 5 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 36 C ORN A 5 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 37 O ORN A 5 0.000 0.000 0.000 1.00 0.00 O 70: HETATM 38 CB ORN A 5 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 39 CG ORN A 5 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 40 CD ORN A 5 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 41 NE ORN A 5 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 42 N LEU A 6 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 43 CA LEU A 6 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 44 C LEU A 6 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 45 O LEU A 6 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 46 CB LEU A 6 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 47 CG LEU A 6 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 48 CD1 LEU A 6 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 49 CD2 LEU A 6 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 50 N DPN A 7 0.000 0.000 0.000 1.00 0.00 N 70: HETATM 51 CA DPN A 7 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 52 C DPN A 7 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 53 O DPN A 7 0.000 0.000 0.000 1.00 0.00 O 70: HETATM 54 CB DPN A 7 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 55 CG DPN A 7 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 56 CD1 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 57 CD2 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 58 CE1 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 59 CE2 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 60 CZ DPN A 7 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 61 N PRO A 8 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 62 CA PRO A 8 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 63 C PRO A 8 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 64 O PRO A 8 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 65 CB PRO A 8 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 66 CG PRO A 8 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 67 CD PRO A 8 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 68 N VAL A 9 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 69 CA VAL A 9 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 70 C VAL A 9 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 71 O VAL A 9 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 72 CB VAL A 9 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 73 CG1 VAL A 9 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 74 CG2 VAL A 9 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 75 N ORN A 10 0.000 0.000 0.000 1.00 0.00 N 70: HETATM 76 CA ORN A 10 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 77 C ORN A 10 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 78 O ORN A 10 0.000 0.000 0.000 1.00 0.00 O 70: HETATM 79 CB ORN A 10 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 80 CG ORN A 10 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 81 CD ORN A 10 0.000 0.000 0.000 1.00 0.00 C 70: HETATM 82 NE ORN A 10 0.000 0.000 0.000 1.00 0.00 N 70: CONECT 1 2 77 70: CONECT 2 3 5 70: CONECT 3 4 4 9 70: CONECT 5 6 70: CONECT 6 7 8 70: CONECT 9 10 70: CONECT 10 11 13 70: CONECT 11 12 12 20 70: CONECT 13 14 70: CONECT 14 15 15 16 70: CONECT 15 17 70: CONECT 16 18 18 70: CONECT 17 19 19 70: CONECT 18 19 70: CONECT 20 21 26 70: CONECT 21 22 24 70: CONECT 22 23 23 27 70: CONECT 24 25 70: CONECT 25 26 70: CONECT 27 28 70: CONECT 28 29 31 70: CONECT 29 30 30 34 70: CONECT 31 32 33 70: CONECT 34 35 70: CONECT 35 36 38 70: CONECT 36 37 37 42 70: CONECT 38 39 70: CONECT 39 40 70: CONECT 40 41 70: CONECT 42 43 70: CONECT 43 44 46 70: CONECT 44 45 45 50 70: CONECT 46 47 70: CONECT 47 48 49 70: CONECT 50 51 70: CONECT 51 52 54 70: CONECT 52 53 53 61 70: CONECT 54 55 70: CONECT 55 56 56 57 70: CONECT 56 58 70: CONECT 57 59 59 70: CONECT 58 60 60 70: CONECT 59 60 70: CONECT 61 62 67 70: CONECT 62 63 65 70: CONECT 63 64 64 68 70: CONECT 65 66 70: CONECT 66 67 70: CONECT 68 69 70: CONECT 69 70 72 70: CONECT 70 71 71 75 70: CONECT 72 73 74 70: CONECT 75 76 70: CONECT 76 77 79 70: CONECT 77 78 78 70: CONECT 79 80 70: CONECT 80 81 70: CONECT 81 82 70: END 70: 70: Sequence: GREG 70: HELM: PEPTIDE1{G.R.E.G}$$$$ 70: Smiles: N=C(N)NCCCC(NC(=O)CN)C(=O)NC(CCC(=O)O)C(=O)NCC(=O)O 70: PDB: 70: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 23 OD1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 24 OD2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 70: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 70: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 70: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 70: CONECT 1 2 70: CONECT 2 3 70: CONECT 3 4 4 5 70: CONECT 5 6 70: CONECT 6 7 9 70: CONECT 7 8 8 16 70: CONECT 9 10 70: CONECT 10 11 70: CONECT 11 12 70: CONECT 12 13 70: CONECT 13 14 14 15 70: CONECT 16 17 70: CONECT 17 18 20 70: CONECT 18 19 19 25 70: CONECT 20 21 70: CONECT 21 22 70: CONECT 22 23 23 24 70: CONECT 25 26 70: CONECT 26 27 70: CONECT 27 28 28 29 70: END 70: 60/222 Test #67: testMolWriter .......................... Passed 0.76 sec 61/222 Test #70: testSequence ........................... Passed 0.15 sec test 71 Start 71: testExtendedStereoParsing 71: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing 71: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 71: Test timeout computed to be: 1500 test 72 Start 72: fileParsersCatchTest 72: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 72: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 72: Test timeout computed to be: 1500 62: Test 62: 62: lostStereoAnd.sdf 62: 62: Test 62: 62: DoubleBondChain.sdf 62: 62: Test 62: 62: UnitsError.sdf 62: 62: Test 62: 62: StarAtom.sdf 62: 62: Test 62: 62: nonProprietary.mol 62: 62: Test 62: 62: ChiralTest.sdf 62: 62: Test 62: 62: TestBond1.mol 62: 62: Test 62: 62: Sgroup_MUL_ParentInMiddle.sdf 62: 62: Test 62: 62: Cubane.mrv 62: 62: Test 62: 62: NewChiralTest.mrv 62: 62: Test 62: 62: NewChiralTest.mrv 62: 62: Test 62: 62: NewChiralTestNoChiral.mrv 62: 62: Test 62: 62: NewChiralTestNoChiral.mrv 62: 62: Test 62: 62: NewChiralTestAllChiral.mrv 62: 62: Test 62: 62: NewChiralTestAllChiral.mrv 62: 62: Test 62: 62: lostStereoAnd.mrv 62: 62: Test 62: 62: DoubleBondChain.mrv 62: 62: Test 62: 62: WigglyAndCrossed.mrv 62: 62: Test 62: 62: BondTypes.mrv 62: 62: Test 62: 62: EmbeddedSGroupSUP_MUL.mrv 62: 62: Test 62: 62: EmbeddedSgroupCOP_SUP.mrv 62: 62: Test 62: 62: EmbeddedSgroupDAT_SUP.mrv 62: 62: Test 62: 62: EmbeddedSgroupMULTICENTER_SUP.mrv 62: 62: Test 62: 62: EmbeddedSgroupMUL_MUL.mrv 62: 62: Test 62: 62: EmbeddedSgroupMUL_MUL2.mrv 62: 62: Test 62: 62: EmbeddedSgroupMUL_SUP.mrv 62: 62: Test 62: 62: EmbeddedSgroupSRU_SUP.mrv 62: 62: Test 62: 62: EmbeddedSgroupSUPEXP_SUP.mrv 62: 62: Test 62: 62: EmbeddedSgroupSUPEXP_SUP2.mrv 62: 62: Test 62: 62: EmbeddedSgroupSUP_MULTICENTER.mrv 62: 62: Test 62: 62: EmbeddedSgroupSUP_SUP.mrv 62: 62: Test 62: 62: EmbeddedSgroupSUP_SUP2.mrv 62: 62: Test 62: 62: RgroupBad.mrv 62: 62: Test 62: 62: valenceLessThanDrawn.mrv 62: 62: Test 62: 62: data_sgroup_no_fieldname.mrv 62: 62: Test 62: 62: data_sgroup_empty_field_data.mrv 62: 62: Test 62: 62: radical_value.mrv 62: 62: Test 62: 62: emptyOneLineAtomList.mrv 62: 62: Test 62: 62: mrvValence_value.mrv 62: 62: Test 62: 62: ChiralTest2.mrv 62: 62: Test 62: 62: ChiralTest.mrv 62: 62: Test 62: 62: SnCl2.mrv 62: 62: Test 62: 62: SnH2Cl2.mrv 62: 62: Test 62: 62: marvin01.mrv 62: 62: Test 62: 62: marvin02.mrv 62: 62: Test 62: 62: marvin07.mrv 62: 62: Test 62: 62: marvin10.mrv 62: 62: Test 62: 62: marvin06.mrv 62: 62: Test 62: 62: marvin12.mrv 62: 62: Test 62: 62: EmptyMol.mrv 62: 62: Test 62: 62: Sparse.mrv 62: 62: Test 62: 62: Sparse2.mrv 62: 62: Test 62: 62: Sparse3.mrv 62: 62: Test 62: 62: MarvinNoCoords.mrv 62: 62: Test 62: 62: aspirin.mrv 62: 62: Test 62: 62: MarvinStereoGroupsZeros.mrv 62: 62: Test 62: 62: MarvinStereoGroupsAbs.mrv 62: 62: Test 62: 62: triphenylphosphine.mrv 62: 62: Test 62: 62: MarvinOldSuperGroupTest.mrv 62: 62: Test 62: 62: RadicalTests.mrv 62: 62: Test 62: 62: AnyBond.mrv 62: 62: Test 62: 62: cisBenzene.mrv 62: 62: Test 62: 62: DativeBond.mrv 62: 62: Test 62: 62: MultipleSgroup.mrv 62: 62: Test 62: 62: SgroupExpanded.mrv 62: 62: Test 62: 62: SgroupMultAttach.mrv 62: 62: Test 62: 62: MarvinMissingX2.mrv 62: 62: Test 62: 62: MarvinMissingY2.mrv 62: 62: Test 62: 62: DataSgroup.mrv 62: 62: Test 62: 62: MulticenterSgroup.mrv 62: 62: [21:31:33] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 62: [21:31:33] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 62/222 Test #71: testExtendedStereoParsing .............. Passed 0.08 sec test 73 Start 73: testPropertyLists 73: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists 73: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 73: Test timeout computed to be: 1500 62: Test 62: 62: GenericSgroup.mrv 62: 62: Test 62: 62: MonomerSgroup.mrv 62: 62: Test 62: 62: modification_sgroup.mrv 62: 62: Test 62: 62: copolymer_sgroup.mrv 62: 62: Test 62: 62: MultipleSgroupParentInMiddleOfAtomBlock.mrv 62: 62: Test 62: 62: EmbeddedSgroups.mrv 62: 62: Test 62: 62: marvin03.mrv 62: 62: Test 62: 62: MarvinBadMissingMolID.mrv 62: 62: [21:31:33] 62: 62: **** 62: Test Assert 62: Expression Failed: 62: Violation occurred on line 309 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp 62: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr 62: **** 62: 62: Test 62: 62: MarvinBadMissingAtomID.mrv 62: 62: Expected id, elementType for an atom definition in MRV file 72: Randomness seeded to: 2360286458 72: [21:31:33] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 72: [21:31:33] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 72: [21:31:33] Could not infer missing lvIdx on malformed SAP line for SGroup 1 72: [21:31:33] SGroup 1 is invalid and will be ignored 72: [21:31:33] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 72: [21:31:33] Could not infer missing lvIdx on malformed SAP line for SGroup 1 72: [21:31:33] SGroup 1 is invalid and will be ignored 72: [21:31:33] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 72: [21:31:33] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 72: [21:31:33] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 72: [21:31:33] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 72: [21:31:33] Could not infer missing lvIdx on malformed SAP line for SGroup 1 72: [21:31:33] SGroup 1 is invalid and will be ignored 72: [21:31:33] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 72: [21:31:33] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 72: [21:31:33] Could not infer missing lvIdx on malformed SAP line for SGroup 1 72: [21:31:33] SGroup 1 is invalid and will be ignored 72: [21:31:33] SGroup 3 referenced on line 40 not found. 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: no bonds 72: Violation occurred on line 139 in file ./Code/GraphMol/SubstanceGroup.cpp 72: Failed Expression: !d_bonds.empty() 72: **** 72: 72: [21:31:33] SGroup 3 referenced on line 40 not found. 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: no bonds 72: Violation occurred on line 139 in file ./Code/GraphMol/SubstanceGroup.cpp 72: Failed Expression: !d_bonds.empty() 72: **** 72: 72: [21:31:33] no bonds 72: [21:31:33] SGroup 1 is invalid and will be ignored 72: [21:31:33] SGroup line too short: 'M SBV 1 6' on line 42 72: [21:31:33] SGroup 1 is invalid and will be ignored 72: [21:31:33] SGroup line too short: 'M SBL 2 3 9 10' on line 46 72: [21:31:33] SGroup 2 is invalid and will be ignored 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: bookmark not found 72: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: bookmark not found 72: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: 72: [21:31:33] bookmark not found 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: bond is not part of the SubstanceGroup 72: Violation occurred on line 158 in file ./Code/GraphMol/SubstanceGroup.cpp 72: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() 72: **** 72: 72: [21:31:33] bond is not part of the SubstanceGroup 72: [21:31:33] SGroup 2 is invalid and will be ignored 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: bookmark not found 72: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: bookmark not found 72: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: 72: [21:31:33] bookmark not found 72: [21:31:33] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. 72: [21:31:33] SGroup 2 is invalid and will be ignored 72: [21:31:33] WARNING: final character of V3000 array is not ')' 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: bookmark not found 72: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: 72: [21:31:33] WARNING: final character of V3000 array is not ')' 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: bookmark not found 72: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: 72: [21:31:33] bookmark not found 72: [21:31:33] SGroup 1 is invalid and will be ignored 72: [21:31:33] WARNING: final character of V3000 array is not ')' 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: bookmark not found 72: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: 72: [21:31:33] WARNING: final character of V3000 array is not ')' 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: bookmark not found 72: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: 72: [21:31:33] bookmark not found 72: [21:31:33] SGroup 1 is invalid and will be ignored 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: bookmark not found 72: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: bookmark not found 72: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: 72: [21:31:33] bookmark not found 72: [21:31:33] SGroup 2 is invalid and will be ignored 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: bookmark not found 72: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: bookmark not found 72: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: 72: [21:31:33] bookmark not found 72: [21:31:33] SGroup 2 is invalid and will be ignored 62: Test 62: 62: MarvinBadX2.mrv 62: 62: The values x2 and y2 must be large floats in MRV file 62: Test 62: 62: MarvinBadY2.mrv 62: 62: The values x2 and y2 must be large floats in MRV file 62: Test 62: 62: MarvinBadStereoGroupsAbs.mrv 62: 62: Unrecognized group definition 62: Test 62: 62: MarvinBadElementType.mrv 62: 62: Test 62: 62: MarvinBadMissingBondID.mrv 62: 62: Test 62: 62: MarvinBadMissingBondAtomRefs 62: 62: Test 62: 62: MarvinBadMissingBondOrder.mrv 62: 62: bond must have one of: order, queryType, or convention in MRV File 72: [21:31:33] Explicit valence for atom # 2 O, 3, is greater than permitted 62: Test 62: 62: MarvinBadMissingSruMolID.mrv 62: 62: Expected a molID in MRV file 72: [21:31:33] Explicit valence for atom # 1 O, 3, is greater than permitted 72: [21:31:33] Explicit valence for atom # 1 C, 5, is greater than permitted 62: Test 62: 62: MarvinBadMissingSruID.mrv 62: 62: Test 62: 62: MarvinBadMissingSruRole.mrv 62: 62: Test 62: 62: MarvinBadMissingSruAtomRef.mrv 62: 62: Test 62: 62: MarvinBadMissingSruTitle.mrv 62: 62: Test 62: 62: MarvinBadSruAtomRef.mrv 62: 62: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 62: Test 62: 62: MarvinBadSruID.mrv 62: 62: Test 62: 62: MarvinBadSruRole.mrv 62: 62: Test 62: 62: MarvinBadSruAtomRef.mrv 62: 62: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 62: Test 62: 62: MarvinBadSruAtomRef.mrv 62: 62: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 62: Test 62: 62: MarvinBadSruConnect.mrv 62: 62: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file 62: Test 62: 62: MarvinBadSupAttachAtom.mrv 62: 62: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 62: Test 62: 62: MarvinBadSupAttachBond.mrv 62: 62: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file 73: Randomness seeded to: 4176488224 73: =============================================================================== 73: All tests passed (95 assertions in 4 test cases) 73: 63/222 Test #73: testPropertyLists ...................... Passed 0.13 sec test 74 Start 74: XYZFileParserCatchTest 74: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest 74: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 74: Test timeout computed to be: 1500 72: [21:31:33] sanitize [21:31:33] UNK: [21:31:33] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 62: Test 62: 62: MarvinBadSupAttachOrder.mrv 62: 62: Order for an AttachmentPoint definition must be an integer in MRV file 62: Test 62: 62: MarvinBadSupAttachAtom.mrv 62: 62: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 62: Test 62: 62: MarvinBadSupAttachAtom.mrv 62: 62: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 62: Test 62: 62: MarvinBadSupAttachAtom.mrv 62: 62: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 62: Test 62: 62: MarvinBadSupMissingAttachBond.mrv 62: 62: No attachment point found for bond to the condensed atom in a superatomSgroup 62: Test 62: 62: MarvinBadSupMissingAttachOrder.mrv 62: 62: Expected atom, order and bond, for an AttachmentPoint definition in MRV file 72: [21:31:33] skipping block at line 7: 'BEGIN ATOM' 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: no stream 72: Violation occurred on line 144 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp 72: Failed Expression: dp_inStream 72: **** 72: 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: no stream 72: Violation occurred on line 179 in file ./Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp 72: Failed Expression: dp_inStream 72: **** 72: 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: no stream 72: Violation occurred on line 427 in file ./Code/GraphMol/FileParsers/SmilesMolSupplier.cpp 72: Failed Expression: dp_inStream 72: **** 72: 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: no stream 72: Violation occurred on line 274 in file ./Code/GraphMol/FileParsers/TDTMolSupplier.cpp 72: Failed Expression: dp_inStream 72: **** 72: 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: no stream 72: Violation occurred on line 515 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 72: Failed Expression: dp_sInStream != nullptr 72: **** 72: 72: [21:31:33] Found a SCD/SED line with missing/empty SDT specification at line 21 72: [21:31:33] Found a SCD/SED line with missing/empty SDT specification at line 20 72: [21:31:33] 72: 72: **** 72: Post-condition Violation 72: Element '' not found 72: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 72: Failed Expression: anum > -1 72: **** 72: 72: [21:31:33] BEGIN SGROUP line not found on line 14 72: [21:31:33] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. 72: [21:31:33] END SGROUP line not found on line 14 72: [21:31:33] END SGROUP line not found on line 14 72: [21:31:33] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. 72: [21:31:33] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. 72: [21:31:33] 72: 72: **** 72: Range Error 72: idx 72: Violation occurred on line 328 in file ./Code/GraphMol/ROMol.cpp 72: Failed Expression: 99 < 9 72: **** 72: 72: [21:31:33] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. 72: [21:31:33] Multiple ATTCHPT values for atom 2 on line 9 74: Randomness seeded to: 305427957 74: =============================================================================== 74: All tests passed (100 assertions in 2 test cases) 74: 64/222 Test #74: XYZFileParserCatchTest ................. Passed 0.05 sec test 75 Start 75: cdxmlParserCatchTest 75: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest 75: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 75: Test timeout computed to be: 1500 72: [21:31:33] Found a SCD/SED line with missing/empty SDT specification at line 12 72: [21:31:33] SMARTS Parse Error: syntax error while parsing: [#6;R 72: [21:31:33] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' 72: [21:31:33] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. 72: [21:31:33] Skipping empty SMARTS value for SMARTSQ. 72: [21:31:33] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. 72: [21:31:33] Found a SCD/SED line with missing/empty SDT specification at line 12 72: [21:31:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 72: [21:31:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 72: [21:31:33] WARNING: Skipping property bar because the value includes an illegal blank line 72: [21:31:33] WARNING: Skipping property baz because the value includes an illegal blank line 72: [21:31:33] WARNING: Skipping property bletch 72: nope because the name includes a newline 72: [21:31:33] WARNING: Skipping property bletch 72: nope2 because the name includes a newline 72: [21:31:33] 72: 72: **** 72: Post-condition Violation 72: Element 'QQQ' not found 72: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 72: Failed Expression: anum > -1 72: **** 72: 72: [21:31:33] 72: 72: **** 72: Post-condition Violation 72: Element 'QQQ' not found 72: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 72: Failed Expression: anum > -1 72: **** 72: 72: [21:31:33] 72: 72: **** 72: Post-condition Violation 72: Element 'QQQ' not found 72: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 72: Failed Expression: anum > -1 72: **** 72: 72: [21:31:33] 72: 72: **** 72: Post-condition Violation 72: Element 'QQQ' not found 72: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 72: Failed Expression: anum > -1 72: **** 72: 72: [21:31:33] atom 3 has a negative isotope value. line: 15 72: [21:31:33] 72: 72: **** 72: Invariant Violation 72: bad prop value 72: Violation occurred on line 158 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 72: Failed Expression: nSwaps < 2 72: **** 72: 72: [21:31:33] 72: 72: **** 72: Pre-condition Violation 72: no input stream 72: Violation occurred on line 480 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 72: Failed Expression: dp_sInStream 72: **** 72: 62: Test 62: 62: marvin03.mrv 62: 62: Test 62: 62: AlexRxn.mrv 62: 62: Test 62: 62: BadReactionSign.mrv 62: 62: Test 62: 62: bondArray_node.mrv 62: 62: Test 62: 62: marvin03.mrv 62: 62: Test 62: 62: marvin04.mrv 62: 62: Test 62: 62: marvin08.mrv 62: 62: Test 62: 62: marvin09.mrv 62: 62: Test 62: 62: marvin11.mrv 62: 62: Test 62: 62: marvin05.mrv 62: 62: Test 62: 62: EmptyRxn.mrv 62: 62: [21:31:33] initialization failed 62: Test 62: 62: RxnNoCoords.mrv 62: 62: Test 62: 62: mrvValenceZero.mrv 62: 62: Test 62: 62: condition_coordinates_mpoint.mrv 62: 62: Test 62: 62: marvin01.mrv 62: 62: Test 62: 62: aspirineSynthesisWithAttributes.mrv 62: 62: Test 62: 62: marvin01.mrv 62: 62: Test 62: 62: NewChiralTest 62: 62: [21:31:33] 62: 62: **** 62: Test Assert 62: Expression Failed: 62: Violation occurred on line 219 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp 62: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr 62: **** 62: 62: terminate called after throwing an instance of 'Invar::Invariant' 62: what(): Expression Failed: 65/222 Test #62: testMrvToMol ...........................Subprocess aborted***Exception: 1.96 sec Using new chirality perception Test NewChiralTest.sdf Test NewChiralTest.sdf Test NewChiralTestNoChiral.sdf Test NewChiralTestNoChiral.sdf Test NewChiralTestAllChiral.sdf Test NewChiralTestAllChiral.sdf Test ProblemShort.mol [21:31:32] For a MultipleSgroup expansion, the matching orphaned bond was not found The multiple sgroup will be ignored Test lostStereoAnd.sdf Test DoubleBondChain.sdf Test UnitsError.sdf Test StarAtom.sdf Test nonProprietary.mol Test ChiralTest.sdf Test TestBond1.mol Test Sgroup_MUL_ParentInMiddle.sdf Test Cubane.mrv Test NewChiralTest.mrv Test NewChiralTest.mrv Test NewChiralTestNoChiral.mrv Test NewChiralTestNoChiral.mrv Test NewChiralTestAllChiral.mrv Test NewChiralTestAllChiral.mrv Test lostStereoAnd.mrv Test DoubleBondChain.mrv Test WigglyAndCrossed.mrv Test BondTypes.mrv Test EmbeddedSGroupSUP_MUL.mrv Test EmbeddedSgroupCOP_SUP.mrv Test EmbeddedSgroupDAT_SUP.mrv Test EmbeddedSgroupMULTICENTER_SUP.mrv Test EmbeddedSgroupMUL_MUL.mrv Test EmbeddedSgroupMUL_MUL2.mrv Test EmbeddedSgroupMUL_SUP.mrv Test EmbeddedSgroupSRU_SUP.mrv Test EmbeddedSgroupSUPEXP_SUP.mrv Test EmbeddedSgroupSUPEXP_SUP2.mrv Test EmbeddedSgroupSUP_MULTICENTER.mrv Test EmbeddedSgroupSUP_SUP.mrv Test EmbeddedSgroupSUP_SUP2.mrv Test RgroupBad.mrv Test valenceLessThanDrawn.mrv Test data_sgroup_no_fieldname.mrv Test data_sgroup_empty_field_data.mrv Test radical_value.mrv Test emptyOneLineAtomList.mrv Test mrvValence_value.mrv Test ChiralTest2.mrv Test ChiralTest.mrv Test SnCl2.mrv Test SnH2Cl2.mrv Test marvin01.mrv Test marvin02.mrv Test marvin07.mrv Test marvin10.mrv Test marvin06.mrv Test marvin12.mrv Test EmptyMol.mrv Test Sparse.mrv Test Sparse2.mrv Test Sparse3.mrv Test MarvinNoCoords.mrv Test aspirin.mrv Test MarvinStereoGroupsZeros.mrv Test MarvinStereoGroupsAbs.mrv Test triphenylphosphine.mrv Test MarvinOldSuperGroupTest.mrv Test RadicalTests.mrv Test AnyBond.mrv Test cisBenzene.mrv Test DativeBond.mrv Test MultipleSgroup.mrv Test SgroupExpanded.mrv Test SgroupMultAttach.mrv Test MarvinMissingX2.mrv Test MarvinMissingY2.mrv Test DataSgroup.mrv Test MulticenterSgroup.mrv [21:31:33] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 [21:31:33] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 Test GenericSgroup.mrv Test MonomerSgroup.mrv Test modification_sgroup.mrv Test copolymer_sgroup.mrv Test MultipleSgroupParentInMiddleOfAtomBlock.mrv Test EmbeddedSgroups.mrv Test marvin03.mrv Test MarvinBadMissingMolID.mrv [21:31:33] **** Test Assert Expression Failed: Violation occurred on line 309 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr **** Test MarvinBadMissingAtomID.mrv Expected id, elementType for an atom definition in MRV file Test MarvinBadX2.mrv The values x2 and y2 must be large floats in MRV file Test MarvinBadY2.mrv The values x2 and y2 must be large floats in MRV file Test MarvinBadStereoGroupsAbs.mrv Unrecognized group definition Test MarvinBadElementType.mrv Test MarvinBadMissingBondID.mrv Test MarvinBadMissingBondAtomRefs Test MarvinBadMissingBondOrder.mrv bond must have one of: order, queryType, or convention in MRV File Test MarvinBadMissingSruMolID.mrv Expected a molID in MRV file Test MarvinBadMissingSruID.mrv Test MarvinBadMissingSruRole.mrv Test MarvinBadMissingSruAtomRef.mrv Test MarvinBadMissingSruTitle.mrv Test MarvinBadSruAtomRef.mrv AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent Test MarvinBadSruID.mrv Test MarvinBadSruRole.mrv Test MarvinBadSruAtomRef.mrv AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent Test MarvinBadSruAtomRef.mrv AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent Test MarvinBadSruConnect.mrv Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file Test MarvinBadSupAttachAtom.mrv Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file Test MarvinBadSupAttachBond.mrv Bond specification for an AttachmentPoint definition must be in the bond array in MRV file Test MarvinBadSupAttachOrder.mrv Order for an AttachmentPoint definition must be an integer in MRV file Test MarvinBadSupAttachAtom.mrv Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file Test MarvinBadSupAttachAtom.mrv Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file Test MarvinBadSupAttachAtom.mrv Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file Test MarvinBadSupMissingAttachBond.mrv No attachment point found for bond to the condensed atom in a superatomSgroup Test MarvinBadSupMissingAttachOrder.mrv Expected atom, order and bond, for an AttachmentPoint definition in MRV file Test marvin03.mrv Test AlexRxn.mrv Test BadReactionSign.mrv Test bondArray_node.mrv Test marvin03.mrv Test marvin04.mrv Test marvin08.mrv Test marvin09.mrv Test marvin11.mrv Test marvin05.mrv Test EmptyRxn.mrv [21:31:33] initialization failed Test RxnNoCoords.mrv Test mrvValenceZero.mrv Test condition_coordinates_mpoint.mrv Test marvin01.mrv Test aspirineSynthesisWithAttributes.mrv Test marvin01.mrv Test NewChiralTest [21:31:33] **** Test Assert Expression Failed: Violation occurred on line 219 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr **** terminate called after throwing an instance of 'Invar::Invariant' what(): Expression Failed: test 76 Start 76: molfileStereoCatchTest 76: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest 76: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 76: Test timeout computed to be: 1500 72: [21:31:33] ERROR: molecules without atoms cannot be exported to Maestro files. 72: [21:31:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 72: [21:31:33] ERROR: the mol cannot be kekulized, and will not be written to the output file. 72: [21:31:33] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. 72: [21:31:33] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 72: [21:31:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 72: [21:31:33] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 72: [21:31:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 72: =============================================================================== 72: All tests passed (1311 assertions in 87 test cases) 72: 66/222 Test #72: fileParsersCatchTest ................... Passed 0.38 sec test 77 Start 77: connectTheDotsTest 77: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest 77: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 77: Test timeout computed to be: 1500 75: Randomness seeded to: 1291246455 75: [21:31:33] Invalid or missing fragment id from CDXML fragment, assigning new one... 75: [21:31:33] Explicit valence for atom # 3 N, 4, is greater than permitted 75: [21:31:33] CDXMLParser: failed sanitizing skipping fragment 32 75: [21:31:33] Bad bond in CDXML skipping fragment 58... 75: [21:31:33] Invalid or missing fragment id from CDXML fragment, assigning new one... 75: [21:31:33] Bad bond in CDXML skipping fragment 58... 77: Randomness seeded to: 1661721794 77: =============================================================================== 77: All tests passed (8 assertions in 1 test case) 77: 67/222 Test #77: connectTheDotsTest ..................... Passed 0.05 sec test 78 Start 78: testSubstructMatch 78: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 78: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct 78: Test timeout computed to be: 1500 75: [21:31:33] WARNING: not removing hydrogen atom without neighbors 75: [21:31:33] WARNING: not removing hydrogen atom without neighbors 75: [21:31:33] WARNING: not removing hydrogen atom without neighbors 75: [21:31:33] WARNING: not removing hydrogen atom without neighbors 75: [21:31:33] WARNING: not removing hydrogen atom without neighbors 75: [21:31:33] WARNING: not removing hydrogen atom without neighbors 75: [21:31:33] WARNING: not removing hydrogen atom without neighbors 75: [21:31:33] WARNING: not removing hydrogen atom without neighbors 78: ----------------- Test 1 78: Done 78: 78: ----------------- Test 2 78: Done 78: 78: ----------------- Test 3 78: Done 78: 78: ----------------- Test 4 78: Done 78: 78: ----------------- Test 5 78: Done 78: 78: ----------------- Test 5 QueryRoot 78: Done 78: 78: ----------------- Test 6 (Issue71 related) 78: Done 78: 78: ----------------- Testing serial numbers on recursive queries 78: Done 78: 78: [21:31:33] ------------------------------------- 78: [21:31:33] Test multithreading 78: reading molecules 75: [21:31:33] WARNING: not removing hydrogen atom without neighbors 75: [21:31:33] WARNING: not removing hydrogen atom without neighbors 75: [21:31:33] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. 76: Randomness seeded to: 4202804643 76: [21:31:33] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 76: [21:31:33] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 76: [21:31:33] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 76: [21:31:33] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 76: [21:31:33] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 2 ignored 76: =============================================================================== 76: All tests passed (142 assertions in 6 test cases) 76: 75: [21:31:33] Incomplete atom labelling, cannot make bond 75: [21:31:33] Incomplete atom labelling, cannot make bond 68/222 Test #76: molfileStereoCatchTest ................. Passed 0.14 sec test 79 Start 79: substructTestCatch 79: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct/substructTestCatch 79: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct 79: Test timeout computed to be: 1500 78: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 78: processing 78: launch :0 78: launch :1 78: launch :2 78: launch :3 75: [21:31:34] Incomplete atom labelling, cannot make bond 63: [21:31:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 63: [21:31:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 63: [21:31:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 63: [21:31:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 75: [21:31:34] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas 75: [21:31:34] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas 75: [21:31:34] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast 75: [21:31:34] Failed to parse XML fragment 5 node: b attribute: Order: 5 75: =============================================================================== 75: All tests passed (252 assertions in 4 test cases) 75: 69/222 Test #75: cdxmlParserCatchTest ................... Passed 0.43 sec test 80 Start 80: testGenericGroups 80: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups 80: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups 80: Test timeout computed to be: 1500 63: [21:31:34] deprecated group abbreviation ignored on line 24 63: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] 78: done 78: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 78: processing2 78: launch2 :0 78: launch2 :1 78: launch2 :2 78: launch2 :3 63: [21:31:34] 63: 63: **** 63: Post-condition Violation 63: Element 'Mv' not found 63: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 63: Failed Expression: anum > -1 63: **** 63: 78: done 78: preprocessing 3 78: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 78: processing3 78: launch3 :0 78: launch3 :1 78: launch3 :2 78: launch3 :3 78: done 78: [21:31:34] done 78: [21:31:34] ------------------------------------- 78: [21:31:34] Test GitHub issue 15 78: [21:31:34] done 78: [21:31:34] ------------------------------------- 78: [21:31:34] Test GitHub issue 409 78: [21:31:34] done 78: [21:31:34] ------------------------------------- 78: [21:31:34] Test chiral matching 78: [21:31:34] done 78: [21:31:34] ------------------------------------- 78: [21:31:34] Test GitHub issue 688: partially specified chiral substructure queries don't work properly 78: [21:31:34] done 78: [21:31:34] ------------------------------------- 78: [21:31:34] Test dative-bond matching 78: [21:31:34] done 78: [21:31:34] ------------------------------------- 78: [21:31:34] Test cis/trans matching 78: [21:31:34] done 78: [21:31:34] ------------------------------------- 78: [21:31:34] Test cis/trans matching part 2 78: [21:31:34] done 78: [21:31:34] ------------------------------------- 78: [21:31:34] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS 78: [21:31:34] done 78: [21:31:34] ------------------------------------- 78: [21:31:34] Testing matching E/Z against Cis/Trans stereo bonds 78: [21:31:34] 78: 78: **** 78: Pre-condition Violation 78: matches must not be empty 78: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp 78: Failed Expression: !matches.empty() 78: **** 78: 78: [21:31:34] 78: 78: **** 78: Pre-condition Violation 78: matches must not be empty 78: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp 78: Failed Expression: !matches.empty() 78: **** 78: 78: [21:31:34] ------------------------------------- 78: [21:31:34] Test substructure matching with a pathological case for symmetric SSSR 78: [21:31:34] ------------------------------------- 78: [21:31:34] Test isAtomTerminalRGroupOrQueryHydrogen 70/222 Test #78: testSubstructMatch ..................... Passed 0.62 sec test 81 Start 81: testReaction 81: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction 81: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions 81: Test timeout computed to be: 1500 79: Randomness seeded to: 296539194 79: =============================================================================== 79: All tests passed (143 assertions in 7 test cases) 79: 71/222 Test #79: substructTestCatch ..................... Passed 0.62 sec test 82 Start 82: testReactionFingerprints 82: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints 82: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions 82: Test timeout computed to be: 1500 82: [21:31:34] ------------------------------------- 82: [21:31:34] Test Reaction StructuralFingerprint 82: [21:31:34] ------------------------------------- 82: [21:31:34] Test Reaction DifferenceFingerprint 72/222 Test #82: testReactionFingerprints ............... Passed 0.07 sec test 83 Start 83: testEnumeration 83: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration 83: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions 83: Test timeout computed to be: 1500 81: smi: O=C1CNC(=O)CN1 81: 1: O=C1CNC(=O)CN1 81: 2: COOC 81: [21:31:34] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] 81: [21:31:34] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 81: O=C1CNC(=O)CN1 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] mapped atoms in the reactants were not mapped in the products. 81: unmapped numbers are: 4 81: [21:31:34] atom 0 in product 0 has multiple charge specifications. 81: mass: 15.0001 81: Oc1ccccn1 81: Oc1ccc[nH]1 81: [21:31:34] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] 81: [21:31:34] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' 81: [21:31:34] SMARTS Parse Error: syntax error while parsing: ([C:2] 81: [21:31:34] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' 81: [21:31:34] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] 81: [21:31:34] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' 81: [21:31:34] SMARTS Parse Error: syntax error while parsing: [C:2]) 81: [21:31:34] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' 81: [21:31:34] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] 81: [21:31:34] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 81: [21:31:34] reactant 2 has no mapped atoms. 80: Randomness seeded to: 2575342414 80: =============================================================================== 80: All tests passed (9408 assertions in 38 test cases) 80: 73/222 Test #80: testGenericGroups ...................... Passed 0.76 sec test 84 Start 84: rxnTestCatch 84: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch 84: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions 84: Test timeout computed to be: 1500 81: [21:31:34] >> Atoms within one molecule have different RXN roles. 81: [21:31:34] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. 81: [21:31:34] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] 81: [21:31:34] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' 81: [21:31:34] SMARTS Parse Error: syntax error while parsing: ([C:2] 81: [21:31:34] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' 81: [21:31:34] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) 81: [21:31:34] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' 81: [21:31:34] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] 81: [21:31:34] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' 81: [21:31:34] reactant 0 has no mapped atoms. 81: [21:31:34] reactant 1 has no mapped atoms. 81: [21:31:34] reactant 3 has no mapped atoms. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 3 found multiple times. 81: [21:31:34] product atom-mapping number 4 found multiple times. 81: [21:31:34] product atom-mapping number 5 found multiple times. 81: [21:31:34] product atom-mapping number 6 found multiple times. 81: [21:31:34] product atom-mapping number 7 found multiple times. 81: [21:31:34] product atom-mapping number 8 found multiple times. 81: [21:31:34] product atom-mapping number 12 found multiple times. 81: [21:31:34] product atom-mapping number 9 found multiple times. 81: [21:31:34] product atom-mapping number 10 found multiple times. 81: [21:31:34] product atom-mapping number 11 found multiple times. 81: [21:31:34] reactant 0 has no mapped atoms. 81: [21:31:34] reactant 1 has no mapped atoms. 81: [21:31:34] reactant 3 has no mapped atoms. 81: [21:31:34] reactant atom-mapping number 19 found multiple times. 81: [21:31:34] reactant atom-mapping number 25 found multiple times. 81: [21:31:34] reactant atom-mapping number 20 found multiple times. 81: [21:31:34] reactant atom-mapping number 21 found multiple times. 81: [21:31:34] reactant atom-mapping number 22 found multiple times. 81: [21:31:34] reactant atom-mapping number 23 found multiple times. 81: [21:31:34] reactant atom-mapping number 24 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br 81: [21:31:34] product atom-mapping number 5 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 3 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 4 found multiple times. 81: [21:31:34] product atom-mapping number 5 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 3 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 4 found multiple times. 81: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br 81: [21:31:34] product atom-mapping number 5 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 3 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 4 found multiple times. 81: [21:31:34] product atom-mapping number 5 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 3 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 4 found multiple times. 81: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 3 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 4 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 3 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 4 found multiple times. 81: F[C@@](Cl)(Br)O[C@](F)(Cl)Br 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 3 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 4 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 3 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 4 found multiple times. 81: F[C@](Cl)(Br)O[C@](F)(Cl)Br 81: [21:31:34] product atom-mapping number 4 found multiple times. 81: [21:31:34] product atom-mapping number 3 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 4 found multiple times. 81: [21:31:34] product atom-mapping number 3 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 4 found multiple times. 81: [21:31:34] product atom-mapping number 3 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 4 found multiple times. 81: [21:31:34] product atom-mapping number 3 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] product atom-mapping number 3 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] mapped atoms in the reactants were not mapped in the products. 81: unmapped numbers are: 4 81: [21:31:34] product atom-mapping number 3 found multiple times. 81: [21:31:34] product atom-mapping number 2 found multiple times. 81: [21:31:34] product atom-mapping number 1 found multiple times. 81: [21:31:34] mapped atoms in the reactants were not mapped in the products. 81: unmapped numbers are: 4 81: [21:31:34] product atom-mapping number 6 not found in reactants. 81: [21:31:34] product atom-mapping number 7 not found in reactants. 81: [21:31:34] product atom-mapping number 8 not found in reactants. 81: [21:31:34] product atom-mapping number 7 not found in reactants. 81: [21:31:34] product atom-mapping number 8 not found in reactants. 81: [21:31:34] product atom-mapping number 9 not found in reactants. 81: [21:31:34] product atom-mapping number 10 not found in reactants. 81: [21:31:34] mapped atoms in the reactants were not mapped in the products. 81: unmapped numbers are: 6 81: [21:31:34] product atom-mapping number 7 not found in reactants. 81: [21:31:34] product atom-mapping number 8 not found in reactants. 81: [21:31:34] product atom-mapping number 9 not found in reactants. 81: [21:31:34] product atom-mapping number 10 not found in reactants. 81: [21:31:34] mapped atoms in the reactants were not mapped in the products. 81: unmapped numbers are: 6 81: smi1 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 81: smi2 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 83: 30000000 30000000 84: Randomness seeded to: 3468707764 84: [21:31:35] atom 0 in product 0 has multiple charge specifications. 84: [21:31:35] Found a SCD/SED line with missing/empty SDT specification at line 34 84: [21:31:35] Found a SCD/SED line with missing/empty SDT specification at line 36 84: [21:31:35] Found a SCD/SED line with missing/empty SDT specification at line 38 84: [21:31:35] Found a SCD/SED line with missing/empty SDT specification at line 40 84: [21:31:35] Found a SCD/SED line with missing/empty SDT specification at line 42 84: [21:31:35] Found a SCD/SED line with missing/empty SDT specification at line 87 84: [21:31:35] Found a SCD/SED line with missing/empty SDT specification at line 89 84: [21:31:35] Found a SCD/SED line with missing/empty SDT specification at line 91 84: [21:31:35] Found a SCD/SED line with missing/empty SDT specification at line 93 84: [21:31:35] Found a SCD/SED line with missing/empty SDT specification at line 95 84: [21:31:35] mapped atoms in the reactants were not mapped in the products. 84: unmapped numbers are: 2 84: [21:31:35] mapped atoms in the reactants were not mapped in the products. 84: unmapped numbers are: 2 84: [21:31:35] SMARTS Parse Error: unclosed ring for input: 'CC1' 84: [21:31:35] SMILES Parse Error: unclosed ring for input: 'CC1' 84: [21:31:35] mapped atoms in the reactants were not mapped in the products. 84: unmapped numbers are: 2 84: [21:31:35] product atom-mapping number 2 not found in reactants. 84: [21:31:35] mapped atoms in the reactants were not mapped in the products. 84: unmapped numbers are: 2 84: [21:31:35] product atom-mapping number 2 not found in reactants. 84: [21:31:35] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 84: =============================================================================== 84: All tests passed (568 assertions in 20 test cases) 84: 74/222 Test #84: rxnTestCatch ........................... Passed 0.15 sec test 85 Start 85: pyChemReactions 85: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" 85: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap 85: Test timeout computed to be: 1500 81: [21:31:35] mapped atoms in the reactants were not mapped in the products. 81: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 81: [21:31:35] product atom-mapping number 17 not found in reactants. 81: [21:31:35] product atom-mapping number 18 not found in reactants. 81: [21:31:35] mapped atoms in the reactants were not mapped in the products. 81: unmapped numbers are: 12 81: [21:31:35] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 81: [21:31:35] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 81: 81: [21:31:35] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels 81: ------------- 81: CCOc1ccccc1 25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 75/222 Test #85: pyChemReactions ........................***Exception: SegFault 0.32 sec test 86 Start 86: pyChemReactionEnumerations 86: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" 86: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap 86: Test timeout computed to be: 1500 81: [21:31:35] reactant 0 has no mapped atoms. 81: [21:31:35] product 0 has no mapped atoms. 81: [21:31:35] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. 76/222 Test #81: testReaction ........................... Passed 1.04 sec test 87 Start 87: pyChemReactionSanitize 87: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" 87: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap 87: Test timeout computed to be: 1500 77/222 Test #86: pyChemReactionEnumerations .............***Exception: SegFault 0.50 sec test 88 Start 88: testChemTransforms 88: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms 88: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms 88: Test timeout computed to be: 1500 25: All 191 tests passed 78/222 Test #37: hanoiTest .............................. Passed 5.86 sec test 89 Start 89: chemTransformsTestCatch 89: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 89: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms 89: Test timeout computed to be: 1500 88: 1 smi: CC 88: 1 smi: CC 88: 2 smi: CCO[C@H](N)P 88: 2 smi: CC 88: replaceSub smi1:CCP(CC)[C@@H](N)O 88: replaceSub smi1:CCNCC 88: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O 88: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O 89: Randomness seeded to: 2644667147 89: [21:31:35] Incomplete atom labelling, cannot make bond 89: [21:31:35] 89: 89: **** 89: Invariant Violation 89: molzip: bond info already exists for end atom with label:1 89: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 89: Failed Expression: !bond.b 89: **** 89: 79/222 Test #87: pyChemReactionSanitize .................***Exception: SegFault 0.42 sec test 90 Start 90: tautomerQueryTestCatch 90: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch 90: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery 90: Test timeout computed to be: 1500 88: [21:31:36] SMARTS Parse Error: syntax error while parsing: bar 88: [21:31:36] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' 89: [21:31:36] Incomplete atom labelling, cannot make bond 89: [21:31:36] 89: 89: **** 89: Invariant Violation 89: molzip: bond info already exists for end atom with label:1 89: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 89: Failed Expression: !bond.b 89: **** 89: 89: [21:31:36] Incomplete atom labelling, cannot make bond 89: [21:31:36] 89: 89: **** 89: Invariant Violation 89: molzip: bond info already exists for end atom with label:1 89: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 89: Failed Expression: !bond.b 89: **** 89: 89: [21:31:36] Incomplete atom labelling, cannot make bond 89: [21:31:36] Incomplete atom labelling, cannot make bond 89: [21:31:36] Incomplete atom labelling, cannot make bond 89: [21:31:36] 89: 89: **** 89: Invariant Violation 89: molzip: bond info already exists for end atom with label:1 89: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 89: Failed Expression: !bond.b 89: **** 89: 89: [21:31:36] Incomplete atom labelling, cannot make bond 89: [21:31:36] 89: 89: **** 89: Invariant Violation 89: molzip: bond info already exists for end atom with label:1 89: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 89: Failed Expression: !bond.b 89: **** 89: 89: [21:31:36] 89: 89: **** 89: Invariant Violation 89: molzip: zipped Bond already exists, perhaps labels are duplicated 89: Violation occurred on line 742 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 89: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) 89: **** 89: 89: =============================================================================== 89: All tests passed (667 assertions in 7 test cases) 89: 80/222 Test #89: chemTransformsTestCatch ................ Passed 0.14 sec test 91 Start 91: pyTautomerQuery 91: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" 91: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap 91: Test timeout computed to be: 1500 81/222 Test #88: testChemTransforms ..................... Passed 0.17 sec test 92 Start 92: testSubgraphs1 92: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 92: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs 92: Test timeout computed to be: 1500 92: ----------------------- 92: Subgraph retrieval 92: Finished 92: ----------------------- 92: testSubgraphs2a 92: Finished 92: ----------------------- 92: testSubgraphs2 92: Finished 92: ----------------------- 92: Path retrieval 92: Finished 92: ----------------------- 92: Path retrieval2 92: Finished 92: ----------------------- 92: Unique Subgraph retrieval 92: Finished 92: ----------------------- 92: testUniqueSubgraphs2 25: 25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... 90: Randomness seeded to: 2403247418 90: =============================================================================== 90: All tests passed (93 assertions in 13 test cases) 90: 82/222 Test #90: tautomerQueryTestCatch ................. Passed 0.34 sec test 93 Start 93: testSubgraphs2 93: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 93: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs 93: Test timeout computed to be: 1500 93: ----------------------- 93: Test1: pathToSubmol 93: Finished 93: ----------------------- 93: Test2: Atom Environments 93: Finished 93: ----------------------- 93: Test 3: Atom Environments (Extension) 93: Finished 93: ----------------------- 93: Testing github Issue103: stereochemistry and pathToSubmol 93: Finished 93: ----------------------- 93: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 93: Finished 83/222 Test #93: testSubgraphs2 ......................... Passed 0.04 sec test 94 Start 94: subgraphsCatch 94: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch 94: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs 94: Test timeout computed to be: 1500 84/222 Test #39: resMolSupplierTest ..................... Passed 6.21 sec test 95 Start 95: filterCatalogTest 95: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest 95: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog 95: Test timeout computed to be: 1500 85/222 Test #91: pyTautomerQuery ........................***Exception: SegFault 0.33 sec test 96 Start 96: pyFilterCatalog 96: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" 96: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap 96: Test timeout computed to be: 1500 94: Randomness seeded to: 4200387616 94: --------- 94: =============================================================================== 94: All tests passed (11 assertions in 1 test case) 94: 86/222 Test #94: subgraphsCatch ......................... Passed 0.07 sec test 97 Start 97: testFragCatalog 97: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 97: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog 97: Test timeout computed to be: 1500 97: 21 92: Finished 92: ----------------------- 92: testRootedSubgraphs 92: Finished 92: ----------------------- 92: testRootedPaths 92: Finished 87/222 Test #92: testSubgraphs1 ......................... Passed 0.46 sec test 98 Start 98: pyFragCatalog 98: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/rough_test.py" 98: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap 98: Test timeout computed to be: 1500 95: Warning: molecule failed filter 95: Warning: molecule failed filter: reason hzone_phenol_A(479) 95: v = { 95: 0,23}, 95: 1,22}, 95: 2,20}, 95: 3,19}, 95: 4,25}, 95: 5,24}, 95: 6,18}, 95: 7,17}, 95: 8,16}, 95: 9,21}, 95: } 95: match = { 95: 0,23}, 95: 1,22}, 95: 2,20}, 95: 3,19}, 95: 4,25}, 95: 5,24}, 95: 6,18}, 95: 7,17}, 95: 8,16}, 95: 9,21}, 95: } 95: Warning: molecule failed filter 95: Warning: molecule failed filter: reason cyano_imine_B(17) 95: v = { 95: 0,11}, 95: 1,12}, 95: 2,13}, 95: 3,14}, 95: 4,15}, 95: 5,10}, 95: 6,9}, 95: 7,8}, 95: 8,7}, 95: 9,6}, 95: 10,5}, 95: 11,17}, 95: 12,16}, 95: } 95: match = { 95: 0,11}, 95: 1,12}, 95: 2,13}, 95: 3,14}, 95: 4,15}, 95: 5,10}, 95: 6,9}, 95: 7,8}, 95: 8,7}, 95: 9,6}, 95: 10,5}, 95: 11,17}, 95: 12,16}, 95: } 95: Warning: molecule failed filter 95: Warning: molecule failed filter: reason keto_keto_gamma(5) 95: v = { 95: 0,0}, 95: 1,1}, 95: 2,2}, 95: 3,4}, 95: 4,5}, 95: 5,6}, 95: 6,7}, 95: 7,8}, 95: 8,9}, 95: 9,14}, 95: 10,15}, 95: 11,16}, 95: } 95: match = { 95: 0,0}, 95: 1,1}, 95: 2,2}, 95: 3,4}, 95: 4,5}, 95: 5,6}, 95: 6,7}, 95: 7,8}, 95: 8,9}, 95: 9,14}, 95: 10,15}, 95: 11,16}, 95: } 88/222 Test #96: pyFilterCatalog ........................***Exception: SegFault 0.44 sec test 99 Start 99: testDescriptors 99: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors 99: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 99: Test timeout computed to be: 1500 99: [21:31:36] ------------------------------------- 99: [21:31:36] Test Crippen parameter acquisition. 99: [21:31:36] done 99: [21:31:36] ------------------------------------- 99: [21:31:36] Test Crippen calculation. 99: [21:31:36] done 99: [21:31:36] ------------------------------------- 99: [21:31:36] Test Issue262: problems with Crippen calculation from pickles. 99: [21:31:36] done 99: [21:31:36] ------------------------------------- 99: [21:31:36] Test AMW calculation. 99: [21:31:36] done 99: [21:31:36] ------------------------------------- 99: [21:31:36] Test Exact MW calculation. 99: [21:31:36] done 99: [21:31:36] ------------------------------------- 99: [21:31:36] Test Labute ASA descriptors. 99: [21:31:36] done 99: [21:31:36] ------------------------------------- 99: [21:31:36] Test TPSA descriptors. 89/222 Test #95: filterCatalogTest ...................... Passed 0.59 sec test 100 Start 100: testAUTOCORR2D 100: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D 100: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 100: Test timeout computed to be: 1500 11: .................. 11: ---------------------------------------------------------------------- 11: Ran 18 tests in 7.251s 11: 11: OK 99: [21:31:37] done 99: [21:31:37] ------------------------------------- 99: [21:31:37] Test Lipinski parameters. 100: [21:31:37] ---------------------------- 100: start test autocorr2D 90/222 Test #11: pyBV ................................... Passed 7.94 sec test 101 Start 101: testATF 101: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testATF 101: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 101: Test timeout computed to be: 1500 91/222 Test #98: pyFragCatalog ..........................***Exception: SegFault 0.56 sec test 102 Start 102: testBCUT 102: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testBCUT 102: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 102: Test timeout computed to be: 1500 92/222 Test #101: testATF ................................ Passed 0.06 sec test 103 Start 103: testEEM 103: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testEEM 103: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 103: Test timeout computed to be: 1500 102: [21:31:37] ------------------------------------- 102: [21:31:37] Basic BCUT tests. 102: [21:31:37] done 102: [21:31:37] ------------------------------------- 102: [21:31:37] Larger BCUT tests. 103: =>start test EEM 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: 0 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 99: [21:31:37] done 99: [21:31:37] ------------------------------------- 99: [21:31:37] Test VSA descriptors. 99: [21:31:37] done 99: [21:31:37] ------------------------------------- 99: [21:31:37] Test molecular formula calculation. 99: [21:31:37] done 99: [21:31:37] ------------------------------------- 99: [21:31:37] Test Issue 3415534. 99: [21:31:37] done 99: [21:31:37] ------------------------------------- 99: [21:31:37] Test Issue3433771: Bad definition for Crippen atom type O11. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 99: [21:31:37] done 99: [21:31:37] ------------------------------------- 99: [21:31:37] Test multithreading 99: reading molecules 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 99: processing 99: launch :0 99: launch :1 99: launch :2 99: launch :3 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: 100 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: [21:31:37] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 63: [21:31:37] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 97: [21:31:37] 97: 97: **** 97: Invariant Violation 97: nonsense 97: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 97: Failed Expression: token != tokens.end() 97: **** 97: 97: [21:31:37] 97: 97: **** 97: Invariant Violation 97: nonsense no new line 97: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 97: Failed Expression: token != tokens.end() 97: **** 97: 97: [21:31:37] 97: 97: **** 97: Invariant Violation 97: nonsense with tab 97: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 97: Failed Expression: token != tokens.end() 97: **** 97: 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 93/222 Test #97: testFragCatalog ........................ Passed 1.15 sec test 104 Start 104: testPBF 104: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testPBF 104: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 104: Test timeout computed to be: 1500 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [21:31:37] ------------------------------------- 104: [21:31:37] Basic PBF tests. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: ---------------------------------- 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: ---------------------------------- 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: [21:31:37] 63: 63: **** 63: Pre-condition Violation 63: rlabel out of range for MDL files 63: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp 63: Failed Expression: rlabel >= 0 && rlabel < 100 63: **** 63: 63: [21:31:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: 200 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: 300 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 102: [21:31:37] ------------------------------------- 102: [21:31:37] Test empty molecule BCUT. 94/222 Test #102: testBCUT ............................... Passed 0.86 sec test 105 Start 105: testRDFcustom 105: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom 105: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 105: Test timeout computed to be: 1500 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [21:31:38] done 104: [21:31:38] ------------------------------------- 104: [21:31:38] PBF edge cases. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 100: [21:31:38] done 100: [21:31:38] ------------------------------------- 100: [21:31:38] Test Github #3806: NaNs from AUTOCORR2D descriptor 100: [21:31:38] done 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [21:31:38] done 95/222 Test #100: testAUTOCORR2D ......................... Passed 1.03 sec test 106 Start 106: testRDF 106: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testRDF 106: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 106: Test timeout computed to be: 1500 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 96/222 Test #104: testPBF ................................ Passed 0.43 sec test 107 Start 107: testMORSE 107: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testMORSE 107: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 107: Test timeout computed to be: 1500 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: [21:31:38] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas 63: [21:31:38] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: 400 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: [21:31:38] Empty atom list: 'M ALS 1 0 F' on line 8. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: de_DE.UTF-8 63: [21:31:38] ------------------------------------- 63: [21:31:38] Test multithreading Locale Switching 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: [21:31:38] Test multithreading (Done) 63: [21:31:38] ------------------------------------- 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: *************************************** 63: *************************************** 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: [21:31:38] bond with order 0 found on line 7. This is not part of the MDL specification. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [21:31:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: Elapsed time: 1.13879 s 103: Errors:0 103: [21:31:38] test on : 500 molecules done 97/222 Test #103: testEEM ................................ Passed 1.19 sec test 108 Start 108: test3D 108: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/test3D 108: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 108: Test timeout computed to be: 1500 63: [21:31:38] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) 63: [21:31:38] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) 63: [21:31:38] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 63: generating smiles 63: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 63: converting back 108: [21:31:38] ------------------------------------- 108: [21:31:38] Basic PMI tests. 63: check isomorphism 108: [21:31:38] done 108: [21:31:38] ------------------------------------- 108: [21:31:38] More PMI/NPR tests. 108: [21:31:38] done 108: [21:31:38] ------------------------------------- 108: [21:31:38] Basic NPR tests. 108: [21:31:38] done 108: [21:31:38] ------------------------------------- 108: [21:31:38] PMI edge cases. 108: [21:31:38] done 108: [21:31:38] ------------------------------------- 108: [21:31:38] NPR edge cases. 108: [21:31:38] done 108: [21:31:38] ------------------------------------- 108: [21:31:38] 3D descriptors. 108: [21:31:38] done 108: [21:31:38] ------------------------------------- 108: [21:31:38] 3D descriptor edge cases. 108: [21:31:38] done 108: [21:31:38] ------------------------------------- 108: [21:31:38] Inertial shape factor. 108: [21:31:38] done 98/222 Test #108: test3D ................................. Passed 0.57 sec test 109 Start 109: testWHIM 109: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testWHIM 109: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 109: Test timeout computed to be: 1500 109: =>start test WHIM 109: [21:31:39] test on : 365 molecules done 99/222 Test #109: testWHIM ............................... Passed 0.46 sec test 110 Start 110: testGETAWAY 110: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 110: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 110: Test timeout computed to be: 1500 63: [21:31:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 63: [21:31:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 63: [21:31:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 63: [21:31:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 63: [21:31:39] deprecated group abbreviation ignored on line 24 63: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] 63: [21:31:39] 63: 63: **** 63: Post-condition Violation 63: Element 'Mv' not found 63: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 63: Failed Expression: anum > -1 63: **** 63: 105: =>start test rdf custom 105: [21:31:39] test on : 365 molecules done 107: =>start test MORSE 107: =>read file 107: [21:31:39] test on : 365 molecules done 100/222 Test #107: testMORSE .............................. Passed 1.78 sec test 111 Start 111: testAUTOCORR3D 111: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 111: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 111: Test timeout computed to be: 1500 106: =>start test rdf 106: [21:31:40] test on : 365 molecules done 101/222 Test #106: testRDF ................................ Passed 2.82 sec test 112 Start 112: testCoulombMat 112: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat 112: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 112: Test timeout computed to be: 1500 112: ===================== Testing CoulombMat ======================= 112: CM test 1 mat Done 102/222 Test #112: testCoulombMat ......................... Passed 0.07 sec test 113 Start 113: descriptorsTestCatch 113: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch 113: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 113: Test timeout computed to be: 1500 113: Randomness seeded to: 2456120972 113: =============================================================================== 113: All tests passed (482 assertions in 7 test cases) 113: 103/222 Test #113: descriptorsTestCatch ................... Passed 0.12 sec test 114 Start 114: pyMolDescriptors 114: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 114: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/Wrap 114: Test timeout computed to be: 1500 111: =>start test autocorr3D 111: [21:31:41] test on : 365 molecules done 104/222 Test #111: testAUTOCORR3D ......................... Passed 1.28 sec test 115 Start 115: pyMolDescriptors3D 115: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/test3D.py" 115: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/Wrap 115: Test timeout computed to be: 1500 25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 25: All 191 tests passed 105/222 Test #114: pyMolDescriptors .......................***Exception: SegFault 0.38 sec test 116 Start 116: testFingerprints 116: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints 116: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 116: Test timeout computed to be: 1500 106/222 Test #115: pyMolDescriptors3D .....................***Exception: SegFault 0.35 sec test 117 Start 117: testMHFPFingerprint 117: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint 117: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 117: Test timeout computed to be: 1500 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: ------------------- 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: ------------------- 116: Atoms: 116: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: Bonds: 116: 0 0->1 order: 1 conj?: 1 aromatic?: 0 116: 1 1->2 order: 12 conj?: 1 aromatic?: 1 116: 2 2->3 order: 12 conj?: 1 aromatic?: 1 116: 3 3->4 order: 12 conj?: 1 aromatic?: 1 116: 4 4->5 order: 12 conj?: 1 aromatic?: 1 116: 5 5->6 order: 12 conj?: 1 aromatic?: 1 116: 6 6->7 order: 12 conj?: 1 aromatic?: 1 116: 7 7->8 order: 12 conj?: 1 aromatic?: 1 116: 8 8->9 order: 1 conj?: 1 aromatic?: 0 116: 9 8->10 order: 12 conj?: 1 aromatic?: 1 116: 10 10->1 order: 12 conj?: 1 aromatic?: 1 116: 11 7->3 order: 12 conj?: 1 aromatic?: 1 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: ------------------- 116: SMI: Oc1cc2[nH]cnc2c(O)n1 116: Atoms: 116: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: Bonds: 116: 0 0->1 order: 1 conj?: 1 aromatic?: 0 116: 1 1->2 order: 12 conj?: 1 aromatic?: 1 116: 2 2->3 order: 12 conj?: 1 aromatic?: 1 116: 3 3->4 order: 12 conj?: 1 aromatic?: 1 116: 4 4->5 order: 12 conj?: 1 aromatic?: 1 116: 5 5->6 order: 12 conj?: 1 aromatic?: 1 116: 6 6->7 order: 12 conj?: 1 aromatic?: 1 116: 7 7->8 order: 12 conj?: 1 aromatic?: 1 116: 8 8->9 order: 1 conj?: 1 aromatic?: 0 116: 9 8->10 order: 12 conj?: 1 aromatic?: 1 116: 10 10->1 order: 12 conj?: 1 aromatic?: 1 116: 11 7->3 order: 12 conj?: 1 aromatic?: 1 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: ------------------- 116: 116: SMI: c1(O)cc2[nH]cnc2c(O)n1 116: Atoms: 116: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: Bonds: 116: 0 0->1 order: 1 conj?: 1 aromatic?: 0 116: 1 0->2 order: 12 conj?: 1 aromatic?: 1 116: 2 2->3 order: 12 conj?: 1 aromatic?: 1 116: 3 3->4 order: 12 conj?: 1 aromatic?: 1 116: 4 4->5 order: 12 conj?: 1 aromatic?: 1 116: 5 5->6 order: 12 conj?: 1 aromatic?: 1 116: 6 6->7 order: 12 conj?: 1 aromatic?: 1 116: 7 7->8 order: 12 conj?: 1 aromatic?: 1 116: 8 8->9 order: 1 conj?: 1 aromatic?: 0 116: 9 8->10 order: 12 conj?: 1 aromatic?: 1 116: 10 10->0 order: 12 conj?: 1 aromatic?: 1 116: 11 7->3 order: 12 conj?: 1 aromatic?: 1 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: ------------------- 116: 116: SMI: c1c(O)nc(O)c2c1[nH]cn2 116: Atoms: 116: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 3 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: Bonds: 116: 0 0->1 order: 12 conj?: 1 aromatic?: 1 116: 1 1->2 order: 1 conj?: 1 aromatic?: 0 116: 2 1->3 order: 12 conj?: 1 aromatic?: 1 116: 3 3->4 order: 12 conj?: 1 aromatic?: 1 116: 4 4->5 order: 1 conj?: 1 aromatic?: 0 116: 5 4->6 order: 12 conj?: 1 aromatic?: 1 116: 6 6->7 order: 12 conj?: 1 aromatic?: 1 116: 7 7->8 order: 12 conj?: 1 aromatic?: 1 116: 8 8->9 order: 12 conj?: 1 aromatic?: 1 116: 9 9->10 order: 12 conj?: 1 aromatic?: 1 116: 10 7->0 order: 12 conj?: 1 aromatic?: 1 116: 11 10->6 order: 12 conj?: 1 aromatic?: 1 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: ------------------- 116: 116: SMI: c12cc(O)nc(O)c1nc[nH]2 116: Atoms: 116: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 3 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: Bonds: 116: 0 0->1 order: 12 conj?: 1 aromatic?: 1 116: 1 1->2 order: 12 conj?: 1 aromatic?: 1 116: 2 2->3 order: 1 conj?: 1 aromatic?: 0 116: 3 2->4 order: 12 conj?: 1 aromatic?: 1 116: 4 4->5 order: 12 conj?: 1 aromatic?: 1 116: 5 5->6 order: 1 conj?: 1 aromatic?: 0 116: 6 5->7 order: 12 conj?: 1 aromatic?: 1 116: 7 7->8 order: 12 conj?: 1 aromatic?: 1 116: 8 8->9 order: 12 conj?: 1 aromatic?: 1 116: 9 9->10 order: 12 conj?: 1 aromatic?: 1 116: 10 7->0 order: 12 conj?: 1 aromatic?: 1 116: 11 10->0 order: 12 conj?: 1 aromatic?: 1 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: ------------------- 116: 116: SMI: [nH]1c2cc(O)nc(O)c2nc1 116: Atoms: 116: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 9 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 10 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: Bonds: 116: 0 0->1 order: 12 conj?: 1 aromatic?: 1 116: 1 1->2 order: 12 conj?: 1 aromatic?: 1 116: 2 2->3 order: 12 conj?: 1 aromatic?: 1 116: 3 3->4 order: 1 conj?: 1 aromatic?: 0 116: 4 3->5 order: 12 conj?: 1 aromatic?: 1 116: 5 5->6 order: 12 conj?: 1 aromatic?: 1 116: 6 6->7 order: 1 conj?: 1 aromatic?: 0 116: 7 6->8 order: 12 conj?: 1 aromatic?: 1 116: 8 8->9 order: 12 conj?: 1 aromatic?: 1 116: 9 9->10 order: 12 conj?: 1 aromatic?: 1 116: 10 10->0 order: 12 conj?: 1 aromatic?: 1 116: 11 8->1 order: 12 conj?: 1 aromatic?: 1 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: ------------------- 116: 116: SMI: c1[nH]c2cc(O)nc(O)c2n1 116: Atoms: 116: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 1 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 8 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: Bonds: 116: 0 0->1 order: 12 conj?: 1 aromatic?: 1 116: 1 1->2 order: 12 conj?: 1 aromatic?: 1 116: 2 2->3 order: 12 conj?: 1 aromatic?: 1 116: 3 3->4 order: 12 conj?: 1 aromatic?: 1 116: 4 4->5 order: 1 conj?: 1 aromatic?: 0 116: 5 4->6 order: 12 conj?: 1 aromatic?: 1 116: 6 6->7 order: 12 conj?: 1 aromatic?: 1 116: 7 7->8 order: 1 conj?: 1 aromatic?: 0 116: 8 7->9 order: 12 conj?: 1 aromatic?: 1 116: 9 9->10 order: 12 conj?: 1 aromatic?: 1 116: 10 10->0 order: 12 conj?: 1 aromatic?: 1 116: 11 9->2 order: 12 conj?: 1 aromatic?: 1 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: ------------------- 116: 116: SMI: n1c[nH]c2cc(O)nc(O)c21 116: Atoms: 116: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: [21:31:41] ------------------------------------- 117: [21:31:41] Test MHFP fingerprint encoder initialization 116: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 10 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: Bonds: 116: 0 0->1 order: 12 conj?: 1 aromatic?: 1 116: 1 1->2 order: 12 conj?: 1 aromatic?: 1 116: 2 2->3 order: 12 conj?: 1 aromatic?: 1 116: 3 3->4 order: 12 conj?: 1 aromatic?: 1 116: 4 4->5 order: 12 conj?: 1 aromatic?: 1 116: 5 5->6 order: 1 conj?: 1 aromatic?: 0 116: 6 5->7 order: 12 conj?: 1 aromatic?: 1 116: 7 7->8 order: 12 conj?: 1 aromatic?: 1 116: 8 8->9 order: 1 conj?: 1 aromatic?: 0 116: 9 8->10 order: 12 conj?: 1 aromatic?: 1 116: 10 10->0 order: 12 conj?: 1 aromatic?: 1 116: 11 10->3 order: 12 conj?: 1 aromatic?: 1 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: ------------------- 116: 116: SMI: c12c(cc(O)nc1O)[nH]cn2 116: Atoms: 116: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: Bonds: 116: 0 0->1 order: 12 conj?: 1 aromatic?: 1 116: 1 1->2 order: 12 conj?: 1 aromatic?: 1 116: 2 2->3 order: 12 conj?: 1 aromatic?: 1 116: 3 3->4 order: 1 conj?: 1 aromatic?: 0 116: 4 3->5 order: 12 conj?: 1 aromatic?: 1 116: 5 5->6 order: 12 conj?: 1 aromatic?: 1 116: 6 6->7 order: 1 conj?: 1 aromatic?: 0 116: 7 1->8 order: 12 conj?: 1 aromatic?: 1 116: 8 8->9 order: 12 conj?: 1 aromatic?: 1 116: 9 9->10 order: 12 conj?: 1 aromatic?: 1 116: 10 6->0 order: 12 conj?: 1 aromatic?: 1 116: 11 10->0 order: 12 conj?: 1 aromatic?: 1 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: ------------------- 116: 116: SMI: c1(O)c2c(cc(O)n1)[nH]cn2 116: Atoms: 116: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: Bonds: 116: 0 0->1 order: 1 conj?: 1 aromatic?: 0 116: 1 0->2 order: 12 conj?: 1 aromatic?: 1 116: 2 2->3 order: 12 conj?: 1 aromatic?: 1 116: 3 3->4 order: 12 conj?: 1 aromatic?: 1 116: 4 4->5 order: 12 conj?: 1 aromatic?: 1 116: 5 5->6 order: 1 conj?: 1 aromatic?: 0 116: 6 5->7 order: 12 conj?: 1 aromatic?: 1 116: 7 3->8 order: 12 conj?: 1 aromatic?: 1 116: 8 8->9 order: 12 conj?: 1 aromatic?: 1 116: 9 9->10 order: 12 conj?: 1 aromatic?: 1 116: 10 7->0 order: 12 conj?: 1 aromatic?: 1 116: 11 10->2 order: 12 conj?: 1 aromatic?: 1 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: ------------------- 116: 116: SMI: Oc1c2c(cc(O)n1)[nH]cn2 116: Atoms: 116: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: Bonds: 116: 0 0->1 order: 1 conj?: 1 aromatic?: 0 116: 1 1->2 order: 12 conj?: 1 aromatic?: 1 116: 2 2->3 order: 12 conj?: 1 aromatic?: 1 116: 3 3->4 order: 12 conj?: 1 aromatic?: 1 116: 4 4->5 order: 12 conj?: 1 aromatic?: 1 116: 5 5->6 order: 1 conj?: 1 aromatic?: 0 116: 6 5->7 order: 12 conj?: 1 aromatic?: 1 116: 7 3->8 order: 12 conj?: 1 aromatic?: 1 116: 8 8->9 order: 12 conj?: 1 aromatic?: 1 116: 9 9->10 order: 12 conj?: 1 aromatic?: 1 116: 10 7->1 order: 12 conj?: 1 aromatic?: 1 116: 11 10->2 order: 12 conj?: 1 aromatic?: 1 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: ------------------- 116: 116: SMI: n1c(O)cc2[nH]cnc2c1O 116: Atoms: 116: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 6 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 116: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 10 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 116: Bonds: 116: 0 0->1 order: 12 conj?: 1 aromatic?: 1 116: 1 1->2 order: 1 conj?: 1 aromatic?: 0 116: 2 1->3 order: 12 conj?: 1 aromatic?: 1 116: 3 3->4 order: 12 conj?: 1 aromatic?: 1 116: 4 4->5 order: 12 conj?: 1 aromatic?: 1 116: 5 5->6 order: 12 conj?: 1 aromatic?: 1 116: 6 6->7 order: 12 conj?: 1 aromatic?: 1 116: 7 7->8 order: 12 conj?: 1 aromatic?: 1 116: 8 8->9 order: 12 conj?: 1 aromatic?: 1 116: 9 9->10 order: 1 conj?: 1 aromatic?: 0 116: 10 9->0 order: 12 conj?: 1 aromatic?: 1 116: 11 8->4 order: 12 conj?: 1 aromatic?: 1 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: ------------------- 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: ------------------- 116: 116: 116: 116: 116: 116: 116: 116: 116: 116: ------------------- 116: 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test Morgan Fingerprints. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test Morgan Fingerprints using fromAtoms argument. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test Morgan Fingerprints as bit vects. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test Morgan Fingerprints with feature invariants. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test additional Morgan fingerprints options. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test Atom Codes. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test Atom Pairs. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test Atom Pairs part 2. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test Topological Torsions. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test Bulk Topological Torsions. 117: [21:31:41] done 117: [21:31:41] ------------------------------------- 117: [21:31:41] Test MHFP shingling creation 117: [21:31:41] done 117: [21:31:41] ------------------------------------- 117: [21:31:41] Test MHFP hashing of string and uint arrays 117: [21:31:41] done 117: [21:31:41] ------------------------------------- 117: [21:31:41] Test SECFP fingerprint functionality 117: [21:31:41] done 107/222 Test #117: testMHFPFingerprint .................... Passed 0.10 sec test 118 Start 118: testFingerprintGenerators 118: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators 118: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 118: Test timeout computed to be: 1500 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test atom-pair fp generator 25: 25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test Hashed Atom Pairs. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test Hashed torsions. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test Rooted Atom Pairs. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test ignoring atoms in Atom Pairs. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test Rooted Topological Torsions. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test ignoring atoms in Topological Torsions. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test atom info from morgan fingerprints. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test atom info from morgan fingerprints including Info Redundant Environments. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] ------------------------------------- 116: [21:31:41] ------------------------------------- 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test atom-pair fp generator with different arguments 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation 116: [21:31:41] ------------------------------------- 116: [21:31:41] ------------------------------------- 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test Atom Pairs including info about chirality. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test Topological Torsions including info about chirality. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test GitHub Issue 25: fingerprint backwards compatibility. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test GitHub Issue 151: PatternFingerprint problems 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test 3D atom pairs. 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule 116: [21:31:41] done 116: [21:31:41] ------------------------------------- 116: [21:31:41] Test multithreading with the pattern FP 116: reading molecules 105: =>start test morse custom 105: [21:31:41] test on : 365 molecules done 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test atom-pair additional output 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test Folded Atom Pairs. 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test Rooted Atom Pairs. 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test ignoring atoms in Atom Pairs. 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test Atom Pairs including info about chirality. 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test Morgan Fingerprints. 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test morgan fp generator 116: pass 1 116: launch :0 116: launch :1 116: launch :2 116: launch :3 66: [21:31:41] Finished: testSmiCorrectness() 66: [21:31:41] ----------------------------------------- 66: 66: [21:31:41] 66: ----------------------------------------- 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test Morgan Fingerprints using fromAtoms argument. 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test Morgan Fingerprints as bit vects. 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test Morgan Fingerprints with feature invariants. 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test additional Morgan fingerprints options. 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Single atoms setting radius 1 bits in Morgan fingerprints 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test different invariant generator combinations 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test invariant overriding 118: [21:31:41] done 118: [21:31:41] ------------------------------------- 118: [21:31:41] Test RDKit fp generator 66: [21:31:41] Spurious data before the first property will be ignored 66: [21:31:41] Property will be truncated after the first blank line 66: [21:31:41] Property will be truncated after the first blank line 66: [21:31:41] Property will be truncated after the first blank line 116: pass 2 116: launch :0 116: launch :1 116: launch :2 116: launch :3 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test Issue252: Bad definitions for Crippen atom types. 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test calculation of ChiVs. 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test calculation of ChiNs. 118: [21:31:42] done 118: [21:31:42] ------------------------------------- 118: [21:31:42] Test unfolded version of RDKFP 118: [21:31:42] ------------------------------------- 118: [21:31:42] Test topological torsion fp generator 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test calculation of HallKierAlpha. 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test calculation of Kappa1. 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test calculation of Kappa2. 118: [21:31:42] done 118: [21:31:42] ------------------------------------- 118: [21:31:42] Test Topological Torsions. 118: [21:31:42] done 118: [21:31:42] ------------------------------------- 118: [21:31:42] Test Folded torsions. 118: [21:31:42] done 118: [21:31:42] ------------------------------------- 118: [21:31:42] Test Bulk Topological Torsions. 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test calculation of Kappa3. 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test Crippen atom type calculations. 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test ring descriptors 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test other count descriptors. 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test MQN 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test GitHub Issue 56. 99: [21:31:42] WARNING: not removing hydrogen atom without neighbors 99: [21:31:42] WARNING: not removing hydrogen atom without neighbors 99: [21:31:42] WARNING: not removing hydrogen atom without neighbors 99: [21:31:42] WARNING: not removing hydrogen atom without neighbors 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test Github92: Bad Crippen atom type for pyrrole H. 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test Github362: order dependence in Kier-Hall descriptors. 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test calculation of spiro and bridgehead counts. 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test Github694: ExactMolWt ignoring the mass of the electron 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Testing Properties and KitchenSink 99: [21:31:42] ---Caught keyerror (bad property name)--- 99: [21:31:42] ---Caught stereo value error--- 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test USR Descriptor 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test Github #1973: support P and S terms for TPSA calculation 99: [21:31:42] done 99: [21:31:42] ------------------------------------- 99: [21:31:42] Test Github #2948: Empty molecule has non-zero LabuteASA 99: [21:31:42] done 105: =>start test AUTOCORR3D custom 105: [21:31:42] test on : 365 molecules done 108/222 Test #99: testDescriptors ........................ Passed 5.44 sec test 119 Start 119: fpTestCatch 119: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 119: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 119: Test timeout computed to be: 1500 66: [21:31:42] Finished: testSDCorrectness() 66: [21:31:42] ----------------------------------------- 66: 109/222 Test #66: testMultithreadedMolSupplier ........... Passed 9.81 sec test 120 Start 120: fpGenTestCatch 120: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch 120: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 120: Test timeout computed to be: 1500 119: Randomness seeded to: 2188200842 119: 119: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 119: fpTestCatch is a Catch2 v3.4.0 host application. 119: Run with -? for options 119: 119: ------------------------------------------------------------------------------- 119: TopologicalTorsionGenerator bit info 119: unfolded bitInfo 119: ------------------------------------------------------------------------------- 119: ./Code/GraphMol/Fingerprints/catch_tests.cpp:473 119: ............................................................................... 119: 119: ./Code/GraphMol/Fingerprints/catch_tests.cpp:500: FAILED: 119: CHECK( *ao.bitPaths == expected ) 119: with expansion: 119: { {?}, {?} } == { {?}, {?} } 119: 119: ------------------------------------------------------------------------------- 119: TopologicalTorsionGenerator bit info 119: unfolded atomToBits atomCounts 119: ------------------------------------------------------------------------------- 119: ./Code/GraphMol/Fingerprints/catch_tests.cpp:504 119: ............................................................................... 119: 119: ./Code/GraphMol/Fingerprints/catch_tests.cpp:533: FAILED: 119: CHECK( *ao.atomToBits == expected1 ) 119: with expansion: 119: { { 142622752 (0x8804020) }, { 142622752 (0x8804020), 8405025 (0x804021) }, { 119: 142622752 (0x8804020), 8405025 (0x804021) }, { 142622752 (0x8804020), 8405025 119: (0x804021) }, { 8405025 (0x804021) } } 119: == 119: { { 4437590048 (0x108804020) }, { 4437590048 (0x108804020), 30073176097 119: (0x700804021) }, { 4437590048 (0x108804020), 30073176097 (0x700804021) }, { 119: 4437590048 (0x108804020), 30073176097 (0x700804021) }, { 30073176097 119: (0x700804021) } } 119: 119: =============================================================================== 119: test cases: 14 | 13 passed | 1 failed 119: assertions: 166 | 164 passed | 2 failed 119: 110/222 Test #119: fpTestCatch ............................***Failed 0.10 sec Randomness seeded to: 2188200842 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fpTestCatch is a Catch2 v3.4.0 host application. Run with -? for options ------------------------------------------------------------------------------- TopologicalTorsionGenerator bit info unfolded bitInfo ------------------------------------------------------------------------------- ./Code/GraphMol/Fingerprints/catch_tests.cpp:473 ............................................................................... ./Code/GraphMol/Fingerprints/catch_tests.cpp:500: FAILED: CHECK( *ao.bitPaths == expected ) with expansion: { {?}, {?} } == { {?}, {?} } ------------------------------------------------------------------------------- TopologicalTorsionGenerator bit info unfolded atomToBits atomCounts ------------------------------------------------------------------------------- ./Code/GraphMol/Fingerprints/catch_tests.cpp:504 ............................................................................... ./Code/GraphMol/Fingerprints/catch_tests.cpp:533: FAILED: CHECK( *ao.atomToBits == expected1 ) with expansion: { { 142622752 (0x8804020) }, { 142622752 (0x8804020), 8405025 (0x804021) }, { 142622752 (0x8804020), 8405025 (0x804021) }, { 142622752 (0x8804020), 8405025 (0x804021) }, { 8405025 (0x804021) } } == { { 4437590048 (0x108804020) }, { 4437590048 (0x108804020), 30073176097 (0x700804021) }, { 4437590048 (0x108804020), 30073176097 (0x700804021) }, { 4437590048 (0x108804020), 30073176097 (0x700804021) }, { 30073176097 (0x700804021) } } =============================================================================== test cases: 14 | 13 passed | 1 failed assertions: 166 | 164 passed | 2 failed test 121 Start 121: pyTestGenerator 121: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 121: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap 121: Test timeout computed to be: 1500 118: [21:31:42] done 118: [21:31:42] ------------------------------------- 118: [21:31:42] Test Rooted Topological Torsions. 118: [21:31:42] done 118: [21:31:42] ------------------------------------- 118: [21:31:42] Test ignoring atoms in Topological Torsions. 118: [21:31:42] done 118: [21:31:42] ------------------------------------- 118: [21:31:42] ------------------------------------- 118: [21:31:42] Test Topological Torsions including info about chirality. 118: [21:31:42] done 118: [21:31:42] ------------------------------------- 118: [21:31:42] Test GitHub Issue 25: fingerprint backwards compatibility. 118: [21:31:42] done 118: [21:31:42] ------------------------------------- 118: [21:31:42] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. 118: [21:31:42] done 118: [21:31:42] ------------------------------------- 118: [21:31:42] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 118: [21:31:42] done 118: [21:31:42] ------------------------------------- 118: [21:31:42] Test convenience and bulk fp calculation functions 120: Randomness seeded to: 3580763006 120: =============================================================================== 120: All tests passed (2678 assertions in 4 test cases) 120: 111/222 Test #120: fpGenTestCatch ......................... Passed 0.21 sec test 122 Start 122: pyTestMHFP 122: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 122: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap 122: Test timeout computed to be: 1500 112/222 Test #121: pyTestGenerator ........................***Exception: SegFault 0.34 sec test 123 Start 123: testPartialCharges 123: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 123: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges 123: Test timeout computed to be: 1500 113/222 Test #123: testPartialCharges ..................... Passed 0.03 sec test 124 Start 124: pyPartialCharges 124: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" 124: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap 124: Test timeout computed to be: 1500 114/222 Test #122: pyTestMHFP .............................***Exception: SegFault 0.30 sec test 125 Start 125: testMolTransforms 125: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 125: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms 125: Test timeout computed to be: 1500 63: [21:31:42] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 63: [21:31:42] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 105: =>start test 2 WHIM custom 105: [21:31:42] test on : 365 molecules done 118: [21:31:42] done 118: [21:31:42] ------------------------------------- 118: [21:31:42] Test GitHub Issue #6958 115/222 Test #118: testFingerprintGenerators .............. Passed 1.35 sec test 126 Start 126: pyMolTransforms 126: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" 126: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap 126: Test timeout computed to be: 1500 125: *********************************************************** 125: Testing MolTransforms 125: --------------------------------- 125: test1Canonicalization 125: 125: --------------------------------- 125: testGetSetBondLength 125: 125: --------------------------------- 125: testGetSetAngle 125: 125: --------------------------------- 125: testGetSetDihedral 125: 125: --------------------------------- 125: testGetSetDihedralThroughTripleBond 125: 125: --------------------------------- 125: testGithub1262: PMI descriptors incorrect 125: 125: --------------------------------- 125: testGithub1908: CanonicalizeMol() distorting bond lengths 125: 125: --------------------------------- 125: testGithub4302: native computeCanonicalTransform() generates non-canonical coords 125: 125: --------------------------------- 125: testWeightedCentroid 125: 125: *********************************************************** 116/222 Test #125: testMolTransforms ...................... Passed 0.09 sec test 127 Start 127: testMMFFForceFieldHelpers 127: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 127: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 127: Test timeout computed to be: 1500 127: [21:31:42] ------------------------------------- 127: [21:31:42] Test MMFF atom types. 127: [21:31:43] done 127: [21:31:43] ------------------------------------- 127: [21:31:43] Testing MMFF builder tools. 63: ---------------------------------- 63: ---------------------------------- 63: [21:31:43] 63: 63: **** 63: Pre-condition Violation 63: rlabel out of range for MDL files 63: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp 63: Failed Expression: rlabel >= 0 && rlabel < 100 63: **** 63: 63: [21:31:43] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 127: [21:31:43] done 127: [21:31:43] ------------------------------------- 127: [21:31:43] Testing MMFF builder+minimization. 117/222 Test #124: pyPartialCharges .......................***Exception: SegFault 0.28 sec test 128 Start 128: testMMFFForceFieldHelpersMultiThread 128: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 128: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 128: Test timeout computed to be: 1500 128: [21:31:43] ------------------------------------- 128: [21:31:43] Test MMFF multithreading 128: processing 128: launch :0 128: launch :1 128: launch :2 128: launch :3 128: launch :4 128: launch :5 128: launch :6 128: launch :7 128: launch :8 128: launch :9 128: launch :10 128: launch :11 128: launch :12 128: launch :13 128: launch :14 128: launch :15 128: launch :16 128: launch :17 128: launch :18 128: launch :19 128: launch :20 128: launch :21 128: launch :22 128: launch :23 127: [21:31:43] done 127: [21:31:43] ------------------------------------- 127: [21:31:43] Testing Issue239. 118/222 Test #126: pyMolTransforms ........................***Exception: SegFault 0.39 sec test 129 Start 129: testUFFForceFieldHelpers 129: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers 129: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF 129: Test timeout computed to be: 1500 129: [21:31:43] ------------------------------------- 129: [21:31:43] Test UFF atom labels. 129: [21:31:43] done 129: [21:31:43] ------------------------------------- 129: [21:31:43] Test UFF atom typer. 129: [21:31:43] done 129: [21:31:43] ------------------------------------- 129: [21:31:43] Testing UFF builder tools. 129: [21:31:43] done 129: [21:31:43] ------------------------------------- 129: [21:31:43] Testing UFF builder+minimization. 127: [21:31:43] done 127: [21:31:43] ------------------------------------- 127: [21:31:43] Testing calcEnergy with passed coords. 127: [21:31:43] done 127: [21:31:43] ------------------------------------- 127: [21:31:43] Testing calcGrad. 127: [21:31:43] done 127: [21:31:43] ------------------------------------- 127: [21:31:43] Testing Issue242. 63: [21:31:43] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas 63: [21:31:43] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' 127: [21:31:43] done 127: [21:31:43] ------------------------------------- 127: [21:31:43] Testing github 308: crash during MMFF parameterization . 127: [21:31:43] ------------------------------------- 127: [21:31:43] Testing SFIssue1653802. 63: [21:31:43] Empty atom list: 'M ALS 1 0 F' on line 8. 127: [21:31:43] done 127: [21:31:43] ------------------------------------- 127: [21:31:43] Testing SFIssue2378119. 127: [21:31:43] done 127: [21:31:43] ------------------------------------- 127: [21:31:43] Test MMFF force-field parameter getters. 127: [21:31:43] ------------------------------------- 127: [21:31:43] Test MMFF multithreading 119/222 Test #63: fileParsersTest1 ....................... Passed 11.43 sec test 130 Start 130: testCrystalForceField 130: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField 130: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF 130: Test timeout computed to be: 1500 128: done 127: generating reference data 128: [21:31:43] done 130: ------------------------------------- 130: Test CrystalFF torsional term. 105: =>start test 1 WHIM custom 105: [21:31:43] test on : 365 molecules done 120/222 Test #128: testMMFFForceFieldHelpersMultiThread ... Passed 0.59 sec test 131 Start 131: pyForceFieldHelpers 131: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 131: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 131: Test timeout computed to be: 1500 121/222 Test #130: testCrystalForceField .................. Passed 0.19 sec test 132 Start 132: testDistGeomHelpers 132: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 132: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers 132: Test timeout computed to be: 1500 129: [21:31:43] done 129: [21:31:43] ------------------------------------- 129: [21:31:43] Testing UFF special cases. 129: [21:31:43] UFFTYPER: Unrecognized charge state for atom: 0 129: [21:31:43] done 129: [21:31:43] ------------------------------------- 129: [21:31:43] Testing Issue239. 132: go 132: ------------------------------------- 132: 129: [21:31:43] done 129: [21:31:43] ------------------------------------- 129: [21:31:43] Testing calcEnergy with passed coords. 129: [21:31:43] done 129: [21:31:43] ------------------------------------- 129: [21:31:43] Testing calcGrad. 129: [21:31:43] done 129: [21:31:43] ------------------------------------- 129: [21:31:43] Testing SFIssue1653802. 129: [21:31:43] done 129: [21:31:43] ------------------------------------- 129: [21:31:43] Testing SFIssue2378119. 129: [21:31:43] done 129: [21:31:43] ------------------------------------- 129: [21:31:43] Test UFF force-field parameter getters. 129: [21:31:43] ------------------------------------- 129: [21:31:43] Testing handling missing parameters. 129: [21:31:43] UFFTYPER: Unrecognized hybridization for atom: 0 129: [21:31:43] UFFTYPER: Unrecognized atom type: Cu+1 (0) 129: [21:31:43] UFFTYPER: Unrecognized hybridization for atom: 0 129: [21:31:43] UFFTYPER: Unrecognized atom type: Cu+1 (0) 129: [21:31:44] done 129: [21:31:44] ------------------------------------- 129: [21:31:44] Testing SFIssue3009337. 129: [21:31:44] done 129: [21:31:44] ------------------------------------- 129: [21:31:44] Test UFF multithreading 129: generating reference data 110: =>start test GETAWAY 110: [21:31:44] test on : 365 molecules done 122/222 Test #110: testGETAWAY ............................ Passed 4.81 sec test 133 Start 133: distGeomHelpersCatch 133: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 133: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers 133: Test timeout computed to be: 1500 133: Randomness seeded to: 4263223498 123/222 Test #131: pyForceFieldHelpers ....................***Exception: SegFault 0.70 sec test 134 Start 134: pyDistGeomHelpers 134: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 134: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 134: Test timeout computed to be: 1500 133: [21:31:44] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, [(1 0), (1 0), (1 2.5), (1 0), (1 0), (1 0)] 133: [21:31:44] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 133: [21:31:44] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] 133: [21:31:44] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 133: [21:31:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 133: [21:31:44] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 133: [21:31:44] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 133: [21:31:44] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 133: ----------- 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 133: [21:31:44] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 133: [21:31:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 133: [21:31:44] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] 133: ----------- 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 133: [21:31:44] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 133: ----------- 133: ----------- 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 133: [21:31:44] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 133: [21:31:44] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 133: [21:31:44] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 133: [21:31:44] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 133: [21:31:44] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 133: [21:31:44] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 127: processing 127: launch :0 127: launch :1 127: launch :2 127: launch :3 127: [21:31:44] Rep: 0 Mol:2 127: [21:31:44] Rep: [21:31:44] Rep: 0 Mol:1 127: 0 Mol:3 127: [21:31:44] Rep: 0 Mol:0 127: [21:31:44] Rep: 0 Mol:5 127: [21:31:44] Rep: 0 Mol:9 127: [21:31:44] Rep: 0 Mol:6 127: [21:31:44] Rep: 0 Mol:10 127: [21:31:44] Rep: 0 Mol:4 127: [21:31:44] Rep: 0 Mol:13 127: [21:31:44] Rep: 0 Mol:17 127: [21:31:44] Rep: 0 Mol:8 127: [21:31:44] Rep: 0 Mol:14 127: [21:31:44] Rep: 0 Mol:12 127: [21:31:44] Rep: 0 Mol:18 133: [21:31:44] UFFTYPER: Unrecognized atom type: Pt5+2 (1) 133: [21:31:44] UFFTYPER: Unrecognized atom type: N_5 (2) 133: [21:31:44] UFFTYPER: Unrecognized atom type: N_5 (3) 133: [21:31:44] UFFTYPER: Unrecognized atom type: N_5 (2) 133: [21:31:44] UFFTYPER: Unrecognized atom type: N_5 (3) 127: [21:31:44] Rep: 0 Mol:16 127: [21:31:44] Rep: 0 Mol:7 127: [21:31:44] Rep: 0 Mol:11 127: [21:31:44] Rep: 0 Mol:22 133: [21:31:44] UFFTYPER: Unrecognized charge state for atom: 1 127: [21:31:44] Rep: 0 Mol:15 127: [21:31:44] Rep: 0 Mol:21 124/222 Test #134: pyDistGeomHelpers ......................***Exception: SegFault 0.38 sec test 135 Start 135: testMolAlign 135: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 135: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign 135: Test timeout computed to be: 1500 127: [21:31:44] Rep: 0 Mol:26 127: [21:31:44] Rep: 0 Mol:19 127: [21:31:44] Rep: 0 Mol:20 133: [21:31:44] UFFTYPER: Unrecognized charge state for atom: 1 133: [21:31:44] UFFTYPER: Unrecognized charge state for atom: 1 127: [21:31:44] Rep: 0 Mol:23 127: [21:31:44] Rep: 0 Mol:25 127: [21:31:44] Rep: 0 Mol:30 127: [21:31:44] Rep: 0 Mol:27 127: [21:31:44] Rep: 0 Mol:24 127: [21:31:44] Rep: 0 Mol:31 127: [21:31:44] Rep: 0 Mol:29 127: [21:31:44] Rep: 0 Mol:28 129: processing 129: launch :0 129: launch :1 129: launch :2 129: launch :3 129: [21:31:44] Rep: 0 Mol:1 129: [21:31:44] Rep: 0 Mol:2 129: [21:31:44] Rep: 0 Mol:5 129: [21:31:44] Rep: 0 Mol:3 129: [21:31:44] Rep: 0 Mol:9 129: [21:31:44] Rep: 0 Mol:0 129: [21:31:44] Rep: 0 Mol:13 129: [21:31:44] Rep: 0 Mol:4 129: [21:31:44] Rep: 0 Mol:17 129: [21:31:44] Rep: 0 Mol:6 129: [21:31:44] Rep: 0 Mol:10 129: [21:31:44] Rep: 0 Mol:7 129: [21:31:44] Rep: 0 Mol:11 129: [21:31:44] Rep: 0 Mol:21 129: [21:31:44] Rep: 0 Mol:25 129: [21:31:44] Rep: 0 Mol:15 129: [21:31:44] Rep: 0 Mol:8 129: [21:31:44] Rep: 0 Mol:14 129: [21:31:44] Rep: 0 Mol:19 129: [21:31:44] Rep: 0 Mol:29 129: [21:31:44] Rep: 0 Mol:23 129: [21:31:44] Rep: 0 Mol:27 129: [21:31:44] Rep: 0 Mol:18 129: [21:31:44] Rep: 0 Mol:12 129: [21:31:44] Rep: 0 Mol:16 133: [21:31:44] UFFTYPER: Unrecognized charge state for atom: 5 129: [21:31:44] Rep: 0 Mol:31 129: [21:31:44] Rep: 0 Mol:22 129: [21:31:44] Rep: 0 Mol:26 129: [21:31:44] Rep: 0 Mol:20 133: [21:31:44] UFFTYPER: Unrecognized charge state for atom: 5 129: [21:31:44] Rep: 0 Mol:30 133: [21:31:44] UFFTYPER: Unrecognized charge state for atom: 5 129: [21:31:44] Rep: 0 Mol:24 129: [21:31:44] Rep: 0 Mol:28 127: [21:31:45] Rep: 20 Mol:2 127: [21:31:45] Rep: 20 Mol:6 127: [21:31:45] Rep: 20 Mol:10 127: [21:31:45] Rep: 20 Mol:14 127: [21:31:45] Rep: 20 Mol:18 127: [21:31:45] Rep: 20 Mol:22 127: [21:31:45] Rep: 20 Mol:26 127: [21:31:45] Rep: 20 Mol:30 133: [21:31:45] UFFTYPER: Unrecognized charge state for atom: 6 133: [21:31:45] UFFTYPER: Unrecognized charge state for atom: 6 135: *********************************************************** 135: Testing MolAlign 135: --------------------------------- 135: test1MolAlign 135: 135: --------------------------------- 135: test1GetBestRMS 135: 135: --------------------------------- 135: test1MolWithQueryAlign 135: 135: --------------------------------- 135: test2AtomMap 135: 135: --------------------------------- 135: test3Weights 135: 135: --------------------------------- 135: testIssue241 135: 135: *********************************************************** 125/222 Test #135: testMolAlign ........................... Passed 0.46 sec test 136 Start 136: testO3AAlign 136: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 136: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign 136: Test timeout computed to be: 1500 133: [21:31:45] UFFTYPER: Unrecognized charge state for atom: 6 127: [21:31:45] Rep: 20 Mol:3 127: [21:31:45] Rep: 20 Mol:7 127: [21:31:45] Rep: 20 Mol:11 127: [21:31:45] Rep: 20 Mol:15 127: [21:31:45] Rep: 20 Mol:19 127: [21:31:45] Rep: 20 Mol:23 127: [21:31:45] Rep: 20 Mol:27 127: [21:31:45] Rep: 20 Mol:31 127: [21:31:45] Rep: 20 Mol:0 127: [21:31:45] Rep: 20 Mol:4 127: [21:31:45] Rep: 20 Mol:8 127: [21:31:45] Rep: 20 Mol:12 127: [21:31:45] Rep: 20 Mol:16 127: [21:31:45] Rep: 20 Mol:20 127: [21:31:45] Rep: 20 Mol:24 127: [21:31:45] Rep: 20 Mol:28 127: [21:31:45] Rep: 20 Mol:1 127: [21:31:45] Rep: 20 Mol:5 127: [21:31:45] Rep: 40 Mol:2 127: [21:31:45] Rep: 40 Mol:6 127: [21:31:45] Rep: 40 Mol:10 127: [21:31:45] Rep: 20 Mol:9 127: [21:31:45] Rep: 40 Mol:14 127: [21:31:45] Rep: 20 Mol:13 127: [21:31:45] Rep: 40 Mol:18 127: [21:31:45] Rep: 20 Mol:17 127: [21:31:45] Rep: 40 Mol:22 127: [21:31:45] Rep: 40 Mol:26 127: [21:31:45] Rep: 40 Mol:30 127: [21:31:45] Rep: 20 Mol:21 127: [21:31:45] Rep: 20 Mol:25 127: [21:31:45] Rep: 20 Mol:29 127: [21:31:45] Rep: 60 Mol:2 127: [21:31:45] Rep: 60 Mol:6 127: [21:31:45] Rep: 60 Mol:10 127: [21:31:45] Rep: 60 Mol:14 127: [21:31:45] Rep: 60 Mol:18 127: [21:31:45] Rep: 60 Mol:22 127: [21:31:45] Rep: 60 Mol:26 127: [21:31:45] Rep: 60 Mol:30 127: [21:31:45] Rep: 40 Mol:3 127: [21:31:45] Rep: 40 Mol:7 127: [21:31:45] Rep: 40 Mol:11 127: [21:31:45] Rep: 40 Mol:15 127: [21:31:45] Rep: 40 Mol:19 127: [21:31:45] Rep: 40 Mol:23 127: [21:31:45] Rep: 40 Mol:27 127: [21:31:45] Rep: 40 Mol:31 127: [21:31:45] Rep: 40 Mol:1 127: [21:31:45] Rep: 40 Mol:5 127: [21:31:45] Rep: 40 Mol:9 127: [21:31:45] Rep: 40 Mol:13 127: [21:31:45] Rep: 40 Mol:17 127: [21:31:45] Rep: 40 Mol:21 127: [21:31:45] Rep: 40 Mol:25 127: [21:31:45] Rep: 40 Mol:29 127: [21:31:45] Rep: 40 Mol:0 127: [21:31:45] Rep: 40 Mol:4 127: [21:31:45] Rep: 40 Mol:8 127: [21:31:45] Rep: 40 Mol:12 127: [21:31:45] Rep: 40 Mol:16 127: [21:31:45] Rep: 40 Mol:20 127: [21:31:45] Rep: 40 Mol:24 127: [21:31:45] Rep: 40 Mol:28 127: [21:31:45] Rep: 80 Mol:2 127: [21:31:45] Rep: 80 Mol:6 127: [21:31:45] Rep: 80 Mol:10 127: [21:31:45] Rep: 80 Mol:14 127: [21:31:45] Rep: 80 Mol:18 127: [21:31:45] Rep: 80 Mol:22 127: [21:31:45] Rep: 80 Mol:26 127: [21:31:45] Rep: 80 Mol:30 127: [21:31:45] Rep: 60 Mol:3 127: [21:31:45] Rep: 60 Mol:7 127: [21:31:45] Rep: 60 Mol:11 127: [21:31:45] Rep: 60 Mol:15 127: [21:31:45] Rep: 60 Mol:19 127: [21:31:45] Rep: 60 Mol:23 127: [21:31:45] Rep: 60 Mol:27 127: [21:31:45] Rep: 60 Mol:31 127: [21:31:46] Rep: 60 Mol:1 127: [21:31:46] Rep: 60 Mol:5 127: [21:31:46] Rep: 60 Mol:9 127: [21:31:46] Rep: 60 Mol:13 127: [21:31:46] Rep: 60 Mol:17 127: [21:31:46] Rep: 60 Mol:21 127: [21:31:46] Rep: 60 Mol:25 127: [21:31:46] Rep: 60 Mol:29 129: [21:31:46] Rep: 100 Mol:1 129: [21:31:46] Rep: 100 Mol:5 129: [21:31:46] Rep: 100 Mol:9 129: [21:31:46] Rep: 100 Mol:13 129: [21:31:46] Rep: 100 Mol:17 129: [21:31:46] Rep: 100 Mol:21 129: [21:31:46] Rep: 100 Mol:25 129: [21:31:46] Rep: 100 Mol:29 129: [21:31:46] Rep: 100 Mol:3 129: [21:31:46] Rep: 100 Mol:7 129: [21:31:46] Rep: 100 Mol:11 129: [21:31:46] Rep: 100 Mol:15 129: [21:31:46] Rep: 100 Mol:19 129: [21:31:46] Rep: 100 Mol:23 129: [21:31:46] Rep: 100 Mol:27 129: [21:31:46] Rep: 100 Mol:31 127: [21:31:46] Rep: 60 Mol:0 127: [21:31:46] Rep: 60 Mol:4 127: [21:31:46] Rep: 60 Mol:8 127: [21:31:46] Rep: 60 Mol:12 127: [21:31:46] Rep: 60 Mol:16 127: [21:31:46] Rep: 60 Mol:20 127: [21:31:46] Rep: 60 Mol:24 127: [21:31:46] Rep: 60 Mol:28 129: [21:31:46] Rep: 100 Mol:0 129: [21:31:46] Rep: 100 Mol:4 129: [21:31:46] Rep: 100 Mol:8 129: [21:31:46] Rep: 100 Mol:12 129: [21:31:46] Rep: 100 Mol:16 129: [21:31:46] Rep: 100 Mol:20 129: [21:31:46] Rep: 100 Mol:24 129: [21:31:46] Rep: 100 Mol:2 129: [21:31:46] Rep: 100 Mol:6 129: [21:31:46] Rep: 100 Mol:10 129: [21:31:46] Rep: 100 Mol:14 129: [21:31:46] Rep: 100 Mol:18 129: [21:31:46] Rep: 100 Mol:22 129: [21:31:46] Rep: 100 Mol:26 129: [21:31:46] Rep: 100 Mol:30 129: [21:31:46] Rep: 100 Mol:28 127: [21:31:46] Rep: 80 Mol:3 127: [21:31:46] Rep: 80 Mol:7 127: [21:31:46] Rep: 80 Mol:11 127: [21:31:46] Rep: 80 Mol:15 127: [21:31:46] Rep: 80 Mol:19 127: [21:31:46] Rep: 80 Mol:23 127: [21:31:46] Rep: 80 Mol:27 127: [21:31:46] Rep: 80 Mol:31 127: [21:31:46] Rep: 80 Mol:1 127: [21:31:46] Rep: 80 Mol:5 127: [21:31:46] Rep: 80 Mol:9 127: [21:31:46] Rep: 80 Mol:13 127: [21:31:46] Rep: 80 Mol:17 127: [21:31:46] Rep: 80 Mol:21 127: [21:31:46] Rep: 80 Mol:25 127: [21:31:46] Rep: 80 Mol:29 127: [21:31:46] Rep: 80 Mol:0 127: [21:31:46] Rep: 80 Mol:4 127: [21:31:46] Rep: 80 Mol:8 127: [21:31:46] Rep: 80 Mol:12 127: [21:31:46] Rep: 80 Mol:16 127: [21:31:46] Rep: 80 Mol:20 127: [21:31:46] Rep: 80 Mol:24 127: [21:31:46] Rep: 80 Mol:28 133: [21:31:46] UFFTYPER: Warning: hybridization set to SP3 for atom 6 127: [21:31:46] done 127: [21:31:46] ------------------------------------- 127: [21:31:46] Test MMFF multithreading2 133: [21:31:47] UFFTYPER: Warning: hybridization set to SP3 for atom 6 133: [21:31:47] UFFTYPER: Warning: hybridization set to SP3 for atom 6 133: [21:31:47] UFFTYPER: Warning: hybridization set to SP3 for atom 11 133: [21:31:47] UFFTYPER: Warning: hybridization set to SP3 for atom 11 133: [21:31:47] UFFTYPER: Warning: hybridization set to SP3 for atom 11 129: [21:31:47] done 129: [21:31:47] ------------------------------------- 129: [21:31:47] Test UFF multithreading2 116: [21:31:47] done 116: [21:31:47] ------------------------------------- 116: [21:31:47] Test GitHub Issue 258: Bad pattern fingerprint for query molecule 116: [21:31:48] done 116: [21:31:48] ------------------------------------- 116: [21:31:48] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. 116: [21:31:48] done 116: [21:31:48] ------------------------------------- 116: [21:31:48] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints 116: [21:31:48] done 116: [21:31:48] ------------------------------------- 116: [21:31:48] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 116: [21:31:48] done 116: [21:31:48] ------------------------------------- 116: [21:31:48] Test unfolded version of RDKFP 116: [21:31:48] ------------------------------------- 116: [21:31:48] Test bitinfo of RDKFP 116: 562: [ 2 ], 116: 709: [ 0 1 ], 116: 1118: [ 0 1 2 ], 116: 1183: [ 1 2 ], 116: 1233: [ 0 1 2 ], 116: 1308: [ 0 ], [ 1 ], 116: 1339: [ 2 ], 116: 1728: [ 1 2 ], 116: 1772: [ 0 ], [ 1 ], 116: 1813: [ 0 1 ], 116: ------------ 116: [21:31:48] ------------------------------------- 116: [21:31:48] Single atoms setting radius 1 bits in Morgan fingerprints 116: [21:31:48] done 116: [21:31:48] ------------------------------------- 116: [21:31:48] Github #879: Pattern fingerprint should set bits for single-atom fragments. 116: [21:31:48] done 116: [21:31:48] ------------------------------------- 116: [21:31:48] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms 116: [21:31:48] done 116: [21:31:48] ------------------------------------- 116: [21:31:48] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False 116: [21:31:48] done 116: [21:31:48] ------------------------------------- 116: [21:31:48] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called 116: [21:31:48] done 116: [21:31:48] ------------------------------------- 116: [21:31:48] Github #2115: BitInfo not complete for RDKFingerprint 116: [21:31:48] done 116: [21:31:48] ------------------------------------- 116: [21:31:48] Github #3723: Fingerprint crash for mols with Zero order bonds 116: [21:31:48] done 126/222 Test #116: testFingerprints ....................... Passed 6.61 sec test 137 Start 137: molAlignCatchTest 137: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 137: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign 137: Test timeout computed to be: 1500 137: Randomness seeded to: 4206975765 137: 344678752 127: [21:31:48] done 127: [21:31:48] ------------------------------------- 127: [21:31:48] Test MMFF multithreading3 137: 299879189 105: =>start test GETAWAY custom 105: [21:31:49] test on : 365 molecules done 127/222 Test #105: testRDFcustom .......................... Passed 11.08 sec test 138 Start 138: pyMolAlign 138: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 138: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap 138: Test timeout computed to be: 1500 128/222 Test #138: pyMolAlign .............................***Exception: SegFault 0.67 sec test 139 Start 139: testFeatures 139: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 139: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures 139: Test timeout computed to be: 1500 129: [21:31:49] done 129: [21:31:49] ------------------------------------- 129: [21:31:49] Test UFF multithreading3 139: [21:31:49] ------------------------------------- 139: [21:31:49] AtomType parser testing. 139: [21:31:49] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] 139: [21:31:49] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' 139: [21:31:49] done 139: [21:31:49] ------------------------------------- 139: [21:31:49] FeatureDefinition parser testing. 139: [21:31:49] done 139: [21:31:49] ------------------------------------- 139: [21:31:49] Test pulling feat defs from a string. 139: [21:31:49] done 139: [21:31:49] ------------------------------------- 139: [21:31:49] FeatureDef functionality testing. 139: [21:31:49] done 139: [21:31:49] ------------------------------------- 139: [21:31:49] FeatureFactory testing. 139: [21:31:49] 1 139: [21:31:49] 2 139: [21:31:49] 3 139: [21:31:49] 4 139: [21:31:49] 5 139: [21:31:49] 6 139: [21:31:49] done 139: [21:31:49] ------------------------------------- 139: [21:31:49] Feature Location testing. 139: [21:31:49] done 139: [21:31:49] ------------------------------------- 139: [21:31:49] Test building a FeatureFactory from a file 139: [21:31:49] done 139: [21:31:49] ------------------------------------- 139: [21:31:49] Testing Issue 224. 139: [21:31:49] done 139: [21:31:49] ------------------------------------- 139: [21:31:49] Testing Issue 225. 139: [21:31:49] done 139: [21:31:49] ------------------------------------- 139: [21:31:49] Test Issue346 139: [21:31:49] done 139: [21:31:49] ------------------------------------- 139: [21:31:49] Test Issue347 139: [21:31:49] done 139: [21:31:49] ------------------------------------- 139: [21:31:49] Testing Issue 348. 139: [21:31:49] SMARTS Parse Error: syntax error while parsing: [C[C] 139: [21:31:49] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' 139: [21:31:49] ------------------------------------- 139: [21:31:49] Testing Nested AtomType definitions. 139: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] 139: [21:31:49] ------------------------------------- 139: [21:31:49] Testing Github Issue #252: crash when calling getPos() with no conformer. 139: [21:31:49] expect a precondition failure message below 139: [21:31:49] 139: 139: **** 139: Pre-condition Violation 139: molecule has no conformers 139: Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp 139: Failed Expression: dp_mol->getNumConformers() 139: **** 139: 139: [21:31:49] Done 139: [21:31:49] ------------------------------------- 139: [21:31:49] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() 139: [21:31:49] done 129/222 Test #139: testFeatures ........................... Passed 0.09 sec test 140 Start 140: pyChemicalFeatures 140: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 140: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 140: Test timeout computed to be: 1500 132: building molecules 132: generating reference data 127: [21:31:50] done 127: [21:31:50] ------------------------------------- 127: [21:31:50] Testing github 162: Incorrect SMILES after MMFF parameterization . 127: [21:31:50] done 127: [21:31:50] ------------------------------------- 127: [21:31:50] Testing github 224: crash during MMFF parameterization . 127: [21:31:50] done 127: [21:31:50] ------------------------------------- 127: [21:31:50] Testing github6728: crash due to missing stretch-bend params. 130/222 Test #127: testMMFFForceFieldHelpers .............. Passed 7.80 sec test 141 Start 141: testShapeHelpers 141: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 141: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers 141: Test timeout computed to be: 1500 131/222 Test #140: pyChemicalFeatures .....................***Exception: SegFault 0.95 sec test 142 Start 142: pyShapeHelpers 142: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" 142: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap 142: Test timeout computed to be: 1500 141: *********************************************************** 141: Testing ShapeHelpers 141: --------------------------------- 141: test1Encode 141: 141: --------------------------------- 141: test2Compare 141: 141: --------------------------------- 141: testGithub4364 141: 141: *********************************************************** 132/222 Test #141: testShapeHelpers ....................... Passed 0.14 sec test 143 Start 143: testMolCatalog 143: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 143: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog 143: Test timeout computed to be: 1500 133/222 Test #143: testMolCatalog ......................... Passed 0.09 sec test 144 Start 144: pyMolCatalog 144: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 144: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap 144: Test timeout computed to be: 1500 134/222 Test #142: pyShapeHelpers .........................***Exception: SegFault 0.37 sec test 145 Start 145: moldraw2DTest1 145: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 145: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D 145: Test timeout computed to be: 1500 145: ----------------- Test 1 129: [21:31:51] done 129: [21:31:51] ------------------------------------- 129: [21:31:51] Testing GitHubIssue62. 129: [21:31:51] beta-lactam 39.6387 129: [21:31:51] cyclopropanone 174.698 129: [21:31:51] aziridine 337.986 129: [21:31:51] aziridinone 115.248 129: [21:31:51] isobutene 2.48217 129: [21:31:51] acetone 1.91788 145: file test1_1.svg gave hash 2024041829U not the expected 1617157703U 135/222 Test #144: pyMolCatalog ...........................***Exception: SegFault 0.35 sec test 146 Start 146: moldraw2DTestCatch 146: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 146: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D 146: Test timeout computed to be: 1500 129: [21:31:51] cyclopentanone 10.1648 129: [21:31:51] cyclopropene 99.4921 129: [21:31:51] cyclobutene 41.0156 129: [21:31:51] cyclopropane 267.236 145: file test1_2.svg gave hash 2870923971U not the expected 1799670018U 145: file test1_3.svg gave hash 133635546U not the expected 1405829717U 129: [21:31:51] gamma-lactam 15.7471 145: file test1_4.svg gave hash 2391498639U not the expected 4252277495U 145: file test1_5.svg gave hash 3746760138U not the expected 2811480876U 145: file test1_6.svg gave hash 3385405097U not the expected 2635907956U 145: file test1_7.svg gave hash 996285542U not the expected 3677608850U 145: Done 145: ----------------- Test 2 145: file test2_1.png gave hash 1430958974U not the expected 307437906U 145: file test2_2.png gave hash 849028519U not the expected 610424244U 129: [21:31:51] trans-2,3-diphenylcyclopropan-1-one 203.398 145: Done 145: ----------------- Test 4 145: file test4_1.png gave hash 3753423155U not the expected 1403972924U 145: file test4_1.svg gave hash 2188871666U not the expected 4157966746U 145: Done 145: ----------------- Test 5 146: Randomness seeded to: 3558669798 146: file testAtomTags_1.svg gave hash 732490855U not the expected 3187798125U 146: file testAtomTags_2.svg gave hash 1085873203U not the expected 822910240U 146: file testAtomTags_3.svg gave hash 4222259109U not the expected 2244078420U 145: file test5_1.png gave hash 2608219002U not the expected 1269428339U 145: file test5_1.svg gave hash 1599298648U not the expected 4074479420U 145: file test5_2.png gave hash 4285280372U not the expected 3073694291U 145: file test5_2.svg gave hash 3060847100U not the expected 1125439478U 129: [21:31:51] cis-2,3-diphenylcyclopropan-1-one 206.852 145: file test5_3.png gave hash 1483467617U not the expected 1865192682U 145: file test5_3.svg gave hash 78536282U not the expected 3322548698U 145: Done 145: ----------------- Test 6 (atom labels) 145: file test6_1.svg gave hash 893244114U not the expected 3623418420U 145: [21:31:51] 145: 145: **** 145: Test Assert 145: Expression Failed: 145: Violation occurred on line 1145 in file ./Code/GraphMol/MolDraw2D/test1.cpp 145: Failed Expression: txt.find(">CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C 147: file rxn_test2_2_1.png gave hash 332162405U not the expected 1215378243U 146: [21:31:51] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 146: [21:31:51] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file rxn_test2_2_1.svg gave hash 1799184287U not the expected 2068242269U 147: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>[cH:3]1[cH:2][c:1]([cH:6][cH:5][c:4]1)Cl Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccccc4 Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccc(cc4)Cl 146: file testHandDrawn-1.svg gave hash 2521705022U not the expected 2253418236U 146: [21:31:51] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 146: [21:31:51] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file rxn_test2_2_2.png gave hash 3469883163U not the expected 3645141778U 147: file rxn_test2_2_2.svg gave hash 328158699U not the expected 269990608U 147: 2 Cc1c(cc([nH]1)[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)[C:7](=[O:8])[NH:9][CH2:10][CH2:11]>>CCc1nc(c(n1[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)C)[C:7](=[O:8])[NH:9][CH2:10][CH2:11] Cc1c(cc([nH]1)c2ccccc2)C(=O)NCCN3CCN(C 147: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl 147: 3 [c:1][C:2](=[O:3])[NH:4]CCC[CH2:5][N:6]([CH2:7])[CH2:8]>>[c:1][C:2](=[O:3])[NH:4]C[CH2:5][N:6]([CH2:7])[CH2:8] CCCn1c(c(cc1c2ccccc2)C(=O)NCCCCN3CCN(CC3)c4cccc(c4Cl)Cl)C CCCn1c(c(cc1c2ccccc2)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl)C 146: file testHandDrawn-1.png gave hash 2842666180U not the expected 698316547U 147: file rxn_test2_2_3.png gave hash 2743788873U not the expected 551946805U 147: file rxn_test2_2_3.svg gave hash 2991177755U not the expected 1544919807U 147: 3 [CH3:1]c1c(cc(n1[CH3:2])C(C)(C)C)[C:3]>>[CH3:2]c1c(c(nc(n1)[CH3:1])[C:3])OC Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3cc(n(c3C)C)C(C)(C)C Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3c(c(nc(n3)C)C)OC 147: file rxn_test2_2_4.png gave hash 511459459U not the expected 4234617566U 147: file rxn_test2_2_4.svg gave hash 1479905333U not the expected 2015871327U 147: Done 147: ----------------- Test 3: test reactant highlighting 139/222 Test #148: pyMolDraw2D ............................***Exception: SegFault 0.36 sec test 150 Start 150: pyFMCS 150: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/testFMCS.py" 150: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap 150: Test timeout computed to be: 1500 146: [21:31:51] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 146: [21:31:51] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file rxn_test3_1.png gave hash 115087423U not the expected 4176857511U 137: 3096020182 146: file testHandDrawn-2.svg gave hash 510484619U not the expected 4132716144U 146: [21:31:51] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 146: [21:31:51] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file rxn_test3_1.svg gave hash 3476760062U not the expected 2165658826U 147: Done 147: ----------------- Test 4: some examples from SMARTS in testing 147: draw! 146: file testHandDrawn-2.png gave hash 2659490970U not the expected 1605553248U 146: [21:31:51] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 146: [21:31:51] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 146: file testHandDrawn-3.svg gave hash 796580786U not the expected 4199337510U 146: [21:31:51] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 146: [21:31:51] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 146: file testHandDrawn-3.png gave hash 1581017601U not the expected 2881952238U 146: [21:31:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 146: [21:31:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file rxn_test4_1.png gave hash 1235707918U not the expected 4187207676U 146: file testHandDrawn-4.svg gave hash 2740159575U not the expected 4197407865U 146: [21:31:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 146: [21:31:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file rxn_test4_1.svg gave hash 3965344825U not the expected 3239755313U 147: done 146: file testHandDrawn-4.png gave hash 3411099526U not the expected 3431655453U 147: file rxn_test4_2.png gave hash 3495773560U not the expected 3490081297U 147: file rxn_test4_2.svg gave hash 1880593804U not the expected 4127054729U 147: Done 140/222 Test #147: moldraw2DRxnTest1 ...................... Passed 0.67 sec test 151 Start 151: FMCStest 151: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 151: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test 151: Test timeout computed to be: 1500 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_15113.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_16613.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_30745.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_30861.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_31495.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_34869.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_36158.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_36559.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_37434.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_39147.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_43754.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_44011.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_44158.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_48076.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_48961.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_49648.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_49703.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_51128.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_51343.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_51842.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_54554.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_100_55749.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_17256.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_20244.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_20245.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_30149.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_30499.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_36186.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_39262.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_43966.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_45279.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_48029.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_49064.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_49801.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_50681.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_54039.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58265.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58358.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58866.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10188_60810.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_21358.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_21597.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_30111.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_30349.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_31746.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_31822.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_35220.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_37603.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_37964.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_39508.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_42164.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_42577.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_44072.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_45522.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46700.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46719.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46744.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_48517.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_49087.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_50034.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_51475.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_53483.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_53506.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_54598.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_55614.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_55737.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57090.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57705.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57785.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_58463.txt 151: 151: testChEMBfopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: L_Txt() chembl_II_sets/Target_no_10193_58700.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_61003.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10193_61349.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10260_38526.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10260_50778.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10260_52179.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10260_54285.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_30224.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_31222.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37349.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37369.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37465.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37541.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_38371.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_44314.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_44578.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_45765.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_46281.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_47928.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_50624.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51341.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51662.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51767.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53081.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53396.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53407.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_58823.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_59190.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_60672.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10280_61176.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10434_20905.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30074.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30175.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30423.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10434_31555.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10434_34878.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10434_35926.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10434_42168.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_20859.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_30060.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_30061.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_30606.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_30866.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_31249.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_34921.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_35188.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_36636.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_37466.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_39202.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_43952.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_49345.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_49591.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_49854.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_51416.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_53537.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_58879.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_60679.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_107_61269.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_108_20600.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_108_20859.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_108_30060.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_108_30606.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_108_30866.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_108_31558.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_108_35188.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_108_37466.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_108_43875.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_108_48911.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_108_49591.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_108_49854.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: no_108_57887.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_108_60679.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_108_6857.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_15478.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_20853.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30840.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30862.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30918.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30994.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31014.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31508.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31623.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35003.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35004.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35281.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35957.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_36520.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_36641.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_38586.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_44431.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_45093.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_51302.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_5247.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_52937.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_57198.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_5739.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_10980_6535.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_20205.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_20986.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_30091.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_34698.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_34705.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37038.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37272.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37447.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_38909.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_38953.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_39472.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_45825.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_47179.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_49028.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_49860.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_51984.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_53395.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_53826.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_54121.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_54530.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_55738.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_57725.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11140_58590.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11365_20432.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11365_30331.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11365_37956.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11365_48114.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11365_58566.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11489_34731.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11489_34818.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37318.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37339.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37564.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11489_39504.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11489_39561.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11489_46082.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11489_46089.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11489_47349.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11489_47757.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11489_51593.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11489_54754.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11489_58262.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11489_58958.txt 151: 151: testChEMBL_Txt(fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: ) chembl_II_sets/Target_no_114_16827.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_20503.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_20724.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_30254.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_30321.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_30572.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_31116.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_31281.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_31443.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_34747.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_34920.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_35040.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_36623.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_37136.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_37208.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_38298.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_38554.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_39088.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_39543.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_44049.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_44562.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_45180.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_45867.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_46087.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_46829.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_47546.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_48395.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_50461.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_50765.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_51669.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_52381.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_57231.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_114_58246.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11534_30999.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11534_31021.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11534_31650.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11534_35011.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11534_37014.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11534_44598.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11534_48446.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50614.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50615.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50618.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11534_51950.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11575_31616.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11575_38381.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11575_45757.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11575_46816.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11575_50701.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11575_54049.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11575_57890.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11575_61045.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11631_30194.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11631_31421.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11631_35538.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11631_55727.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11631_60676.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11631_61130.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_11631_6444.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_15623.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_20096.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_21591.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_30184.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_30380.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_30745.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_30861.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_31619.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_34869.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_35284.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_36158.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_36915.txt 151: 151: testChEMBL_Txfopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: t() chembl_II_sets/Target_no_121_37434.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_37541.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_37677.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_38837.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_39530.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_43793.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_44158.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_44164.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_44579.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_44593.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_44692.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_44914.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_45878.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_48050.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_48706.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_48944.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_48961.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_49880.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_50055.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_50512.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_51064.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_53537.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_55749.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_58879.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_121_6876.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12209_44664.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12209_46451.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12209_50640.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12209_56102.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12209_58015.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12209_59089.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12209_59092.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12209_61340.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12252_31458.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12252_38481.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12252_42104.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12252_49475.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12252_49933.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12252_50558.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_126_37249.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_126_39117.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_126_48227.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_126_48229.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_126_53969.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_126_54262.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_126_55353.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_126_61212.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20250.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20506.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20626.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20689.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_21358.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_30158.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_30349.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_34843.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_35220.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_36318.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_36800.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_39349.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_45385.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_45676.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_46700.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_46719.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_48517.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_52690.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_53483.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_55435.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_56102.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_58015.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_12952_58375.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_1295fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: 2_58700.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_13001_16724.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_13001_2710.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_13001_30128.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_13001_31250.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_13001_35519.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_13001_36905.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_13001_46788.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_13001_4737.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_13001_55736.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_13001_57473.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_16146.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_30313.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_30539.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_30653.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_30988.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_31179.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_31339.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_3525.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_36886.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_37020.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_38128.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_43952.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_45210.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_45899.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_47889.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_51800.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_53158.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_5330.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_55648.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_56096.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_57287.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_57399.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_57606.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_58470.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_130_60894.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_15010.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_20304.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_20542.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_20788.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_21358.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_30349.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_31103.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_31764.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_31822.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_35220.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_37964.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_42164.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_44072.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_45522.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_46719.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_46744.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_48416.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_49740.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_50034.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_50640.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_53483.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_53506.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_53814.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_55435.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_56074.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_56107.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_57090.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_57705.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_57785.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_57861.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_58583.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_59089.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_15_59092.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_20600.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_30764.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_34876.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_37427.tfopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: xt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_38266.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_45283.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_46990.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_47123.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_47900.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_48050.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_48062.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_48076.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_50718.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_50972.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_51372.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_51830.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_53049.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_53505.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_54021.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_54565.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_54570.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_57666.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_57890.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_58072.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_58634.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_58643.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_59080.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_59202.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_59346.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_60379.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_60385.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_165_61098.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_17045_31154.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_17045_35648.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_17045_48914.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_17045_51975.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_17045_52435.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_17045_55790.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_17045_58958.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_17045_61146.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20191.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20562.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20606.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20607.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30003.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30402.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30726.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30924.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31457.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31460.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31600.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31620.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31640.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31782.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31797.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31829.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31856.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34690.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34691.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34694.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_35712.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_37497.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_37539.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48070.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48219.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48824.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48902.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_52867.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_53534.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_54570.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_58727.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_60159.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_19905_60661.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_30037.txt 151: 151: testChEMBL_Txt() chefopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: mbl_II_sets/Target_no_259_34734.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_35365.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_35787.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_36793.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_37845.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_38328.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_39374.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_43936.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_44059.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_44405.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_44424.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_45166.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_46158.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_46425.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_47187.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_48435.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_48817.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_48849.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_48957.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_48965.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_49519.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_49921.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_50392.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_50972.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_52405.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_52442.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_53169.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_54640.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_57207.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_58537.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_58920.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_259_60358.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_25_16077.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_25_34943.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_25_36391.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_25_36574.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_25_52906.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_25_54642.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_43_16385.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_43_20333.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_43_20774.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_43_35825.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_43_37637.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_43_47741.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_43_48567.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_43_48841.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_43_49589.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_43_50564.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_43_51201.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_43_53150.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_43_55747.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_43_58276.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_20813.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_2331.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_2391.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_30374.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_30512.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_30796.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_31058.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_31450.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_36609.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_36636.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_38266.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_43800.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_47621.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_49433.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_49550.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_49865.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_51005.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_52373.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_53878.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_54554.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_57508.txtfopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_57618.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_59484.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_51_6563.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_61_16845.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_61_37106.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_61_37272.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_61_47947.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_61_50754.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_61_55800.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_61_57380.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_65_35328.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_65_36137.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_65_38826.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_65_44596.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_65_51275.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_65_55671.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_20155.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_30616.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_30653.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_30988.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_31339.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_31527.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_31631.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_36047.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_36568.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_36636.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_37020.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_38128.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_43952.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_45210.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_47889.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_51064.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_51800.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_5330.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_57508.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_58470.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_72_60894.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_20730.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_20753.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_30097.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_30663.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_35365.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_35375.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_35918.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_36010.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_36780.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_36793.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_37845.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_39110.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_39546.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_43936.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_44405.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_44424.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_44683.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_45166.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_46648.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_46986.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_47070.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_47187.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_48435.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_48817.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_49138.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_49460.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_49519.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_49532.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_49829.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_50608.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_54640.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_87_61082.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_90_15727.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_90_20155.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_90_30407.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_90_3525.txt 151: 151: testChEMBfopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: L_Txt() chembl_II_sets/Target_no_93_12377.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_93_1308.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_93_34759.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_93_35447.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_93_42214.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_93_45877.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_93_47082.txt 151: 151: testChEMBL_Txt() chembl_II_sets/Target_no_93_57082.txt 151: 151: testFileSDF_RandomSet(): benchmark/chembl13-10000-random-pairs.sdf 151: ERROR: RDKit could not load input file 151: 151: testFileSDF_RandomSet(): benchmark/chembl13_pairs.smi 151: ERROR: RDKit could not load input file 151: 151: testFileSDF_RandomSet(): benchmark/chembl13_knearest_2.smi 151: ERROR: RDKit could not load input file 151: 151: testFileSDF_RandomSet(): benchmark/chembl13_knearest_10.smi 151: ERROR: RDKit could not load input file 151: 151: testFileSDF_RandomSet(): benchmark/chembl13_knearest_100.smi 151: ERROR: RDKit could not load input file 151: 151: testFileSDF_RandomSet(): benchmark/chembl13_threshold_80.smi 151: ERROR: RDKit could not load input file 151: 151: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 151: ERROR: RDKit could not load input file 141/222 Test #151: FMCStest ............................... Passed 0.09 sec test 152 Start 152: molHashCatchTest 152: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest 152: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolHash 152: Test timeout computed to be: 1500 142/222 Test #150: pyFMCS .................................***Exception: SegFault 0.39 sec test 153 Start 153: pyMolHash 153: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/Wrap/testMolHash.py" 153: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap 153: Test timeout computed to be: 1500 152: Randomness seeded to: 3604964006 152: =============================================================================== 152: All tests passed (304 assertions in 9 test cases) 152: 143/222 Test #152: molHashCatchTest ....................... Passed 0.13 sec test 154 Start 154: testMMPA 154: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/testMMPA 154: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MMPA 154: Test timeout computed to be: 1500 154: 154: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 154: Time elapsed 0.004750 seconds 154: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 154: 1: NOREF. Reference data NOT LISTED in test case. 154: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 154: 2: NOREF. Reference data NOT LISTED in test case. 154: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] 154: 3: NOREF. Reference data NOT LISTED in test case. 154: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 154: 4: NOREF. Reference data NOT LISTED in test case. 154: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 154: 5: NOREF. Reference data NOT LISTED in test case. 154: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 154: 6: NOREF. Reference data NOT LISTED in test case. 154: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 154: 7: NOREF. Reference data NOT LISTED in test case. 154: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 154: 8: NOREF. Reference data NOT LISTED in test case. 154: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 154: 9: NOREF. Reference data NOT LISTED in test case. 154: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 154: 10: NOREF. Reference data NOT LISTED in test case. 154: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 154: 11: NOREF. Reference data NOT LISTED in test case. 154: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 154: 12: NOREF. Reference data NOT LISTED in test case. 154: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 154: 13: NOREF. Reference data NOT LISTED in test case. 154: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 154: 14: NOREF. Reference data NOT LISTED in test case. 154: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 154: 15: NOREF. Reference data NOT LISTED in test case. 154: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 154: 16: NOREF. Reference data NOT LISTED in test case. 154: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 154: 17: NOREF. Reference data NOT LISTED in test case. 154: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 154: 18: NOREF. Reference data NOT LISTED in test case. 154: 154: --- UNMATCHED Reference RESULTS: --- 154: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 154: ----------------------------------- 154: Time elapsed 0.004319 seconds 154: 154: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 154: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 154: 1: PASSED. matchedRefRes = 4 154: 2: O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21, C[*:1].O=C(NCCO)[*:2] 154: 2: PASSED. matchedRefRes = 1 154: 3: O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OCC[*:2] 154: 3: PASSED. matchedRefRes = 6 154: 4: O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OC[*:2] 154: 4: PASSED. matchedRefRes = 13 154: 5: O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].O[*:2] 154: 5: PASSED. matchedRefRes = 12 154: 6: NULL, Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 154: 6: PASSED. matchedRefRes = 10 154: 7: O=C(N[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 154: 7: NOREF. Reference data NOT LISTED in test case.O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 154: 8: O=C(NC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 154: 8: NOREF. Reference data NOT LISTED in test case.O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 154: 9: O=C(NCC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 154: 9: NOREF. Reference data NOT LISTED in test case.O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 154: 10: NULL, Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 154: 10: PASSED. matchedRefRes = 3 154: 11: C([*:1])[*:2], Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 154: 11: NOREF. Reference data NOT LISTED in test case.C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 154: 12: C(C[*:2])[*:1], Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 154: 12: PASSED. matchedRefRes = 8 154: 13: NULL, Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 154: 13: PASSED. matchedRefRes = 9 154: 14: C([*:1])[*:2], Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 154: 14: PASSED. matchedRefRes = 11 154: 15: NULL, Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 154: 15: PASSED. matchedRefRes = 2 154: 154: --- UNMATCHED Reference RESULTS: --- 154: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 154: 7: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:2] 154: 14: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 154: 15: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 154: ----------------------------------- 154: 154: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 154: Time elapsed 0.004309 seconds 154: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 154: 1: PASSED. matchedRefRes = 4 154: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] 154: 2: PASSED. matchedRefRes = 1 154: 3: res= O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2] 154: 3: PASSED. matchedRefRes = 6 154: 4: res= O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2] 154: 4: PASSED. matchedRefRes = 13 154: 5: res= O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].O[*:2] 154: 5: PASSED. matchedRefRes = 12 154: 6: res= NULL,Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 154: 6: PASSED. matchedRefRes = 10 154: 7: res= O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 154: 7: NOREF. Reference data NOT LISTED in test case. 154: 8: res= O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 154: 8: NOREF. Reference data NOT LISTED in test case. 154: 9: res= O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 154: 9: NOREF. Reference data NOT LISTED in test case. 154: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 154: 10: PASSED. matchedRefRes = 3 154: 11: res= C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 154: 11: NOREF. Reference data NOT LISTED in test case. 154: 12: res= C(C[*:2])[*:1],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 154: 12: PASSED. matchedRefRes = 8 154: 13: res= NULL,Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 154: 13: PASSED. matchedRefRes = 9 154: 14: res= C([*:1])[*:2],Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 154: 14: PASSED. matchedRefRes = 11 154: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 154: 15: PASSED. matchedRefRes = 2 154: 154: --- UNMATCHED Reference RESULTS: --- 154: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 154: 7: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:2] 154: 14: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 154: 15: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 154: ----------------------------------- 154: 154: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE 154: Time elapsed 0.001058 seconds 154: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 154: 1: PASSED. matchedRefRes = 2 154: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] 154: 2: PASSED. matchedRefRes = 3 154: 3: res= C([*:1])([*:2])[*:3],C1CN1[*:3].C[*:1].O=C[*:2] 154: 3: NOREF. Reference data NOT LISTED in test case. 154: 4: res= C1CN1C([*:1])[*:2],C[*:1].O=C[*:2] 154: 4: PASSED. matchedRefRes = 4 154: 5: res= NULL,C1CN1[*:1].CC(C=O)[*:1] 154: 5: PASSED. matchedRefRes = 5 154: 6: res= CC([*:1])[*:2],C1CN1[*:2].O=C[*:1] 154: 6: NOREF. Reference data NOT LISTED in test case. 154: 7: res= NULL,CC(N1CC1)[*:1].O=C[*:1] 154: 7: PASSED. matchedRefRes = 7 154: 154: --- UNMATCHED Reference RESULTS: --- 154: 1: CC(N1CC1)C(=O),Case1-SIMPLE,C([*:1])([*:2])[*:3],C1CN1[*:2].C[*:1].O=C[*:3] 154: 6: CC(N1CC1)C(=O),Case1-SIMPLE,CC([*:1])[*:2],C1CN1[*:1].O=C[*:2] 154: ----------------------------------- 154: 154: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 154: Time elapsed 0.004677 seconds 154: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 154: 1: NOREF. Reference data NOT LISTED in test case. 154: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 154: 2: NOREF. Reference data NOT LISTED in test case. 154: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] 154: 3: NOREF. Reference data NOT LISTED in test case. 154: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 154: 4: NOREF. Reference data NOT LISTED in test case. 154: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 154: 5: NOREF. Reference data NOT LISTED in test case. 154: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 154: 6: NOREF. Reference data NOT LISTED in test case. 154: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 154: 7: NOREF. Reference data NOT LISTED in test case. 154: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 154: 8: NOREF. Reference data NOT LISTED in test case. 154: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 154: 9: NOREF. Reference data NOT LISTED in test case. 154: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 154: 10: NOREF. Reference data NOT LISTED in test case. 154: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 154: 11: NOREF. Reference data NOT LISTED in test case. 154: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 154: 12: NOREF. Reference data NOT LISTED in test case. 154: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 154: 13: NOREF. Reference data NOT LISTED in test case. 154: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 154: 14: NOREF. Reference data NOT LISTED in test case. 154: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 154: 15: NOREF. Reference data NOT LISTED in test case. 154: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 154: 16: NOREF. Reference data NOT LISTED in test case. 154: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 154: 17: NOREF. Reference data NOT LISTED in test case. 154: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 154: 18: NOREF. Reference data NOT LISTED in test case. 154: 154: --- UNMATCHED Reference RESULTS: --- 154: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 154: ----------------------------------- 154: 154: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 154: Time elapsed 0.005210 seconds 154: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 154: 1: NOREF. Reference data NOT LISTED in test case. 154: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 154: 2: NOREF. Reference data NOT LISTED in test case. 154: 3: res= O=C(O[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc(C[*:2])cc1 154: 3: NOREF. Reference data NOT LISTED in test case. 154: 4: res= O=C(O[*:1])C(c1ccccc1)[*:2],O[*:2].c1ccc(C[*:1])cc1 154: 4: NOREF. Reference data NOT LISTED in test case. 154: 5: res= O=C(O[*:1])C([*:2])[*:3],O[*:2].c1ccc(C[*:1])cc1.c1ccc([*:3])cc1 154: 5: NOREF. Reference data NOT LISTED in test case. 154: 6: res= O=C(O[*:1])C(O)[*:2],c1ccc(C[*:1])cc1.c1ccc([*:2])cc1 154: 6: NOREF. Reference data NOT LISTED in test case. 154: 7: res= NULL,O=C(OC[*:1])C(O)c1ccccc1.c1ccc([*:1])cc1 154: 7: NOREF. Reference data NOT LISTED in test case. 154: 8: res= O=C(OC[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc([*:2])cc1 154: 8: NOREF. Reference data NOT LISTED in test case. 154: 9: res= O=C(OC[*:2])C(c1ccccc1)[*:1],O[*:1].c1ccc([*:2])cc1 154: 9: NOREF. Reference data NOT LISTED in test case. 154: 10: res= O=C(OC[*:2])C([*:1])[*:3],O[*:1].c1ccc([*:2])cc1.c1ccc([*:3])cc1 154: 10: NOREF. Reference data NOT LISTED in test case. 154: 11: res= O=C(OC[*:1])C(O)[*:2],c1ccc([*:1])cc1.c1ccc([*:2])cc1 154: 11: NOREF. Reference data NOT LISTED in test case. 154: 12: res= NULL,O=C(OCc1ccccc1)[*:1].OC(c1ccccc1)[*:1] 154: 12: NOREF. Reference data NOT LISTED in test case. 154: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2] 154: 13: NOREF. Reference data NOT LISTED in test case. 154: 14: res= C([*:1])([*:2])[*:3],O=C(OCc1ccccc1)[*:1].O[*:2].c1ccc([*:3])cc1 154: 14: PASSED. matchedRefRes = 1 154: 15: res= OC([*:1])[*:2],O=C(OCc1ccccc1)[*:1].c1ccc([*:2])cc1 154: 15: NOREF. Reference data NOT LISTED in test case. 154: 16: res= NULL,O=C(OCc1ccccc1)C(c1ccccc1)[*:1].O[*:1] 154: 16: NOREF. Reference data NOT LISTED in test case. 154: 17: res= O=C(OCc1ccccc1)C([*:1])[*:2],O[*:1].c1ccc([*:2])cc1 154: 17: NOREF. Reference data NOT LISTED in test case. 154: 18: res= NULL,O=C(OCc1ccccc1)C(O)[*:1].c1ccc([*:1])cc1 154: 18: NOREF. Reference data NOT LISTED in test case. 154: 154: --- ALL PASSED --- 154: ----------------------------------- 154: 5 TEST CASES FAILED 144/222 Test #154: testMMPA ............................... Passed 0.19 sec test 155 Start 155: pyMMPA 155: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/Wrap/testMMPA.py" 155: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap 155: Test timeout computed to be: 1500 145/222 Test #153: pyMolHash ..............................***Exception: SegFault 0.29 sec test 156 Start 156: testRascalMCES 156: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES 156: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES 156: Test timeout computed to be: 1500 25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 137: 852142639 137: =============================================================================== 137: All tests passed (73 assertions in 3 test cases) 137: 146/222 Test #137: molAlignCatchTest ...................... Passed 4.89 sec test 157 Start 157: testRascalCluster 157: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster 157: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES 157: Test timeout computed to be: 1500 147/222 Test #155: pyMMPA .................................***Exception: SegFault 0.38 sec test 158 Start 158: pyMolDraw2D 158: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" 158: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/Wrap 158: Test timeout computed to be: 1500 25: All 191 tests passed 25: 25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... 148/222 Test #158: pyMolDraw2D ............................***Exception: SegFault 0.33 sec test 159 Start 159: testCIPLabeler 159: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler 159: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler 159: Test timeout computed to be: 1500 159: Randomness seeded to: 2140536306 159: [21:31:53] non kekulizable aromatic bond being treated as bond order 1 159: [21:31:53] non kekulizable aromatic bond being treated as bond order 1 159: [21:31:53] non kekulizable aromatic bond being treated as bond order 1 159: [21:31:53] non kekulizable aromatic bond being treated as bond order 1 159: [21:31:53] non kekulizable aromatic bond being treated as bond order 1 159: [21:31:53] non kekulizable aromatic bond being treated as bond order 1 159: =============================================================================== 159: All tests passed (5977 assertions in 13 test cases) 159: 149/222 Test #159: testCIPLabeler ......................... Passed 0.32 sec test 160 Start 160: pyCIPLabelsWrapTest 160: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" 160: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 160: Test timeout computed to be: 1500 146: file testHandDrawn-5a.svg gave hash 3134495213U not the expected 3628607349U 146: [21:31:54] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 146: [21:31:54] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 146: file testHandDrawn-5b.svg gave hash 2824094466U not the expected 2522138089U 146: [21:31:54] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 146: [21:31:54] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 150/222 Test #160: pyCIPLabelsWrapTest ....................***Exception: SegFault 0.63 sec test 161 Start 161: pyCIPLabelsValidation 161: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" 161: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 161: Test timeout computed to be: 1500 146: file testHandDrawn-5.png gave hash 1151078189U not the expected 3439548169U 146: file testBrackets-1a.svg gave hash 2369751903U not the expected 4189399574U 146: file testBrackets-1b.svg gave hash 319778462U not the expected 3773894816U 146: file testBrackets-1c.svg gave hash 2369751903U not the expected 4189399574U 146: file testBrackets-1d.svg gave hash 319778462U not the expected 3773894816U 146: file testBrackets-1e.svg gave hash 3154382550U not the expected 2492125470U 146: file testBrackets-2a.svg gave hash 3500488585U not the expected 1050851904U 146: file testBrackets-2b.svg gave hash 2920281586U not the expected 776446765U 146: file testBrackets-2c.svg gave hash 3500488585U not the expected 1050851904U 146: file testBrackets-2d.svg gave hash 2920281586U not the expected 776446765U 146: file testBrackets-3a.svg gave hash 28453276U not the expected 1374944956U 146: file testBrackets-4a.svg gave hash 194812969U not the expected 3837821771U 146: file testBrackets-4b.svg gave hash 1005379322U not the expected 1477006167U 146: file testBrackets-5a.svg gave hash 2213299352U not the expected 3061667963U 146: file testBrackets-5768.svg gave hash 2420715958U not the expected 2559120196U 146: file testSGroupData-1a.svg gave hash 625253365U not the expected 426096222U 146: file testSGroupData-1b.svg gave hash 1898552060U not the expected 1688385103U 146: file testSGroupData-3a.svg gave hash 4202997715U not the expected 2405789536U 146: file testSGroupData-2a.svg gave hash 1654087185U not the expected 195363059U 146: file testSGroupData-2b.svg gave hash 1776709036U not the expected 942041938U 146: file testSGroupData-3a.svg gave hash 4202997715U not the expected 2405789536U 146: file testPositionVariation-1.svg gave hash 175752745U not the expected 1347003808U 146: file testPositionVariation-1b.svg gave hash 1574891203U not the expected 174339626U 146: file testPositionVariation-2.svg gave hash 3363492135U not the expected 473948585U 146: file testPositionVariation-3.svg gave hash 3172212082U not the expected 4039188982U 146: file testPositionVariation-4.svg gave hash 3544201052U not the expected 3407574474U 146: file testNoAtomLabels-1.svg gave hash 727719523U not the expected 4255907058U 146: file testNoAtomLabels-2.svg gave hash 4176633817U not the expected 3643749531U 146: file testQueryBonds-1a.svg gave hash 1498812112U not the expected 1525751327U 146: file testQueryBonds-1b.svg gave hash 1854448352U not the expected 3339941561U 146: file testQueryBonds-1c.svg gave hash 1282788757U not the expected 375371096U 146: file testQueryBonds-2.svg gave hash 176419118U not the expected 3399320861U 146: file testLinkNodes-2-0.svg gave hash 2135545988U not the expected 145749789U 146: file testLinkNodes-2-30.svg gave hash 3039055224U not the expected 3203923109U 146: file testLinkNodes-2-60.svg gave hash 3035733973U not the expected 2004079267U 146: file testLinkNodes-2-90.svg gave hash 1935416984U not the expected 171994932U 146: file testLinkNodes-2-120.svg gave hash 3176047424U not the expected 673333745U 146: file testLinkNodes-2-150.svg gave hash 4108663686U not the expected 51965551U 146: file testLinkNodes-2-180.svg gave hash 1267063813U not the expected 433020402U 146: file testMolAnnotations-1.svg gave hash 4022064522U not the expected 1638024035U 146: file testMolAnnotations-2a.svg gave hash 100295044U not the expected 3029896996U 146: file testMolAnnotations-2b.svg gave hash 1729540304U not the expected 3110016833U 146: file testMolAnnotations-2c.svg gave hash 3114393753U not the expected 611992302U 146: file testMolAnnotations-3a.svg gave hash 1578731737U not the expected 55379064U 146: file testMolAnnotations-3b.svg gave hash 3914185508U not the expected 936144383U 146: file testMolAnnotations-3c.svg gave hash 613361257U not the expected 3983292921U 146: file testMolAnnotations-3d.svg gave hash 3911959820U not the expected 748075045U 146: file testMolAnnotations-4a.svg gave hash 3377859254U not the expected 3474490519U 146: file testLinkNodes-1-0.svg gave hash 132913310U not the expected 3845035394U 146: file testLinkNodes-1-30.svg gave hash 4167789299U not the expected 3207457801U 146: file testLinkNodes-1-60.svg gave hash 3654538383U not the expected 2620138210U 146: file testLinkNodes-1-90.svg gave hash 2745010131U not the expected 1457485851U 146: file testLinkNodes-1-120.svg gave hash 486328858U not the expected 4267267665U 146: file testLinkNodes-1-150.svg gave hash 3641412484U not the expected 574622776U 146: file testLinkNodes-1-180.svg gave hash 2073805227U not the expected 2541146503U 146: file testGithub3744.svg gave hash 829939430U not the expected 387800653U 146: file testAtomLists-1.svg gave hash 3464470154U not the expected 1887579391U 146: file testAtomLists-2.svg gave hash 802804202U not the expected 555139782U 146: file testIsoDummyIso.svg gave hash 1524400075U not the expected 2405371137U 146: file testNoIsoDummyIso.svg gave hash 3628257665U not the expected 748558214U 146: file testIsoNoDummyIso.svg gave hash 3076357258U not the expected 3054263824U 146: file testNoIsoNoDummyIso.svg gave hash 2664166819U not the expected 1185561148U 146: file testDeuteriumTritium.svg gave hash 3793326464U not the expected 1867318569U 146: file testHydrogenBonds1.svg gave hash 430254599U not the expected 2605974904U 146: [21:31:54] unrecognized bond typefile testHydrogenBonds2.svg gave hash 204416197U not the expected 645414593U 146: file testGithub3912.1.svg gave hash 1559292065U not the expected 2513727029U 146: file testGithub3912.2.svg gave hash 2876399273U not the expected 3814673891U 146: file testGithub2976.svg gave hash 968668044U not the expected 2669316911U 146: file testReactionCoords.svg gave hash 1202163015U not the expected 402445764U 146: file testAnnotationColors.svg gave hash 1685962958U not the expected 2216313312U 146: file testGithub4238_1.svg gave hash 2002583221U not the expected 2621118499U 146: file testGithub4238_1.png gave hash 897433972U not the expected 3410617836U 146: file testGithub4323_1.svg gave hash 2366752113U not the expected 2536621192U 146: file testGithub4323_2.svg gave hash 2788649217U not the expected 2120846759U 146: file testGithub4323_3.svg gave hash 2889173297U not the expected 4156867630U 146: file testGithub4323_4.svg gave hash 1561706994U not the expected 3824125601U 146: file testGithub4323_1.png gave hash 1609227587U not the expected 3723958844U 149: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 149: Time elapsed 0.001 seconds 149: 149: test32() 149: 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 149: Time elapsed 0.129 seconds 149: 149: test190() 149: 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 149: Time elapsed 0.016 seconds 149: 149: test3() 149: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds 149: Time elapsed 0.024 seconds 149: 149: testSimpleFast() 149: 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 149: Time elapsed 0.198 seconds 149: 149: testSimple() 149: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds 149: Time elapsed 0.186 seconds 149: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds 149: Time elapsed 0.183 seconds 149: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds 149: Time elapsed 0.179 seconds 149: 149: testSegFault() 149: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds 149: Time elapsed 0.017 seconds 149: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds 149: Time elapsed 0.020 seconds 149: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1 6 atoms, 6 bonds 149: Time elapsed 0.020 seconds 149: 149: testThreshold() 149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 149: Time elapsed 0.000 seconds 149: 149: testRing1() 149: 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 149: Time elapsed 0.565 seconds 149: 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 149: Time elapsed 0.778 seconds 149: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#7;r6,!R1]:&@[#6;r6,!R1](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds 149: Time elapsed 0.611 seconds 149: 149: testAtomCompareIsotopes() 149: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds 149: Time elapsed 0.009 seconds 149: 149: testAtomCompareAnyAtom() 149: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds 149: Time elapsed 0.000 seconds 149: 149: testAtomCompareAnyAtom() 149: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds 149: Time elapsed 0.000 seconds 149: 149: testAtomCompareAnyAtom() 149: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds 149: Time elapsed 0.001 seconds 149: 149: testAtomCompareAnyAtom() 149: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds 149: Time elapsed 0.000 seconds 149: 149: testJnk1LigandsDistance() 149: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds 149: Time elapsed 0.017 seconds 149: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds 151/222 Test #161: pyCIPLabelsValidation ..................***Exception: SegFault 0.60 sec test 162 Start 162: deprotectTest 162: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 162: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect 162: Test timeout computed to be: 1500 149: Time elapsed 0.002 seconds 149: 149: test18() 149: 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]1 149: 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 149: Time elapsed 0.012 seconds 149: 149: test504() 149: 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]1 149: 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 149: Time elapsed 0.146 seconds 149: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 149: Time elapsed 0.002 seconds 149: 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 149: Time elapsed 0.044 seconds 149: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds 149: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0014 seconds. bond[0]=6 149: STATISTICS: 149: Total Growing Steps = 1, MCS found on 1 step, for 0.0014 seconds 149: Initial Seeds = 1, Mismatched 0 149: Inspected Seeds = 2 149: Rejected by BestSize = 0 149: IndividualBondExcluded = 0 149: MatchCheck Seeds = 2 149: MatchCalls = 2 149: MatchFound = 1 149: fastMatchCalls = 1 149: fastMatchFound = 0 149: slowMatchCalls = 2 149: slowMatchFound = 1 149: DupCacheFound = 0 0 matched, 0 mismatched 149: HashCache size = 1 keys 149: HashCache size = 1 entries 149: FindHashInCache = 2 149: HashFoundInCache= 0 149: ExactMatchCalls = 0 149: ExactMatchFound = 0 149: Time elapsed 0.002 seconds 149: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 149: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 149: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 149: res sub = 1 size=3 149: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds 149: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 149: res sub = 1 size=3 149: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds 149: test target = CC[C@H](F)Cl query = CCC useChirality = 0 149: res sub = 1 size=3 149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 149: test target = CC[C@H](F)Cl query = CCC useChirality = 1 149: res sub = 1 size=3 149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 149: test target = CCC(F)Cl query = CC useChirality = 0 149: res sub = 1 size=2 149: MCS: [#6]-[#6] 2 atoms, 1 bonds 149: test target = CCC(F)Cl query = CC useChirality = 1 149: res sub = 1 size=2 149: MCS: [#6]-[#6] 2 atoms, 1 bonds 149: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 149: res sub = 1 size=4 149: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 149: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 149: res sub = 1 size=4 149: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 149: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 149: res sub = 1 size=4 149: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 149: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 149: res sub = 1 size=4 149: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 149: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 149: res sub = 0 size=0 149: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds 149: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 149: res sub = 0 size=0 149: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds 149: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 149: res sub = 1 size=4 149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 149: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 149: res sub = 1 size=4 149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 149: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 149: res sub = 1 size=4 149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 149: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 149: res sub = 1 size=4 149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 149: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 149: res sub = 1 size=4 149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 149: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 149: res sub = 0 size=0 149: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 149: test target = OC(F)CCl query = OC(F)C useChirality = 0 149: res sub = 1 size=4 149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 149: test target = OC(F)CCl query = OC(F)C useChirality = 1 149: res sub = 1 size=4 149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 149: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 149: res sub = 1 size=4 149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 149: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 149: res sub = 0 size=0 149: MCS: [#9] 1 atoms, 0 bonds 149: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 149: res sub = 1 size=4 149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 149: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 149: res sub = 0 size=0 149: MCS: [#9] 1 atoms, 0 bonds 149: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 149: res sub = 1 size=3 149: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 149: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 149: res sub = 1 size=3 149: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 149: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 149: res sub = 1 size=3 149: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 149: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 149: res sub = 1 size=3 149: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 149: 149: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> 149: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 149: res sub = 1 size=3 149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 149: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 149: res sub = 1 size=3 149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 149: done 162: Randomness seeded to: 2950417715 162: =============================================================================== 162: All tests passed (111 assertions in 3 test cases) 162: 152/222 Test #162: deprotectTest .......................... Passed 0.24 sec test 163 Start 163: pyDeprotect 163: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap/rough_test.py" 163: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap 163: Test timeout computed to be: 1500 153/222 Test #163: pyDeprotect ............................***Exception: SegFault 0.37 sec test 164 Start 164: testReducedGraphs 164: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs 164: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs 164: Test timeout computed to be: 1500 164: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 164: 154/222 Test #164: testReducedGraphs ...................... Passed 0.06 sec test 165 Start 165: pyReducedGraphs 165: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" 165: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap 165: Test timeout computed to be: 1500 132: validating reference data 146: file testGithub4323_3.png gave hash 1164680292U not the expected 2185913679U 146: file testGithub4508_1.svg gave hash 3378775316U not the expected 2047652713U 146: [21:31:55] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 146: file testGithub4508_1b.svg gave hash 860872304U not the expected 2681019776U 155/222 Test #165: pyReducedGraphs ........................***Exception: SegFault 0.35 sec test 166 Start 166: trajectoryTest 166: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest 166: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory 166: Test timeout computed to be: 1500 146: file testGithub4508_2.svg gave hash 1943409269U not the expected 1382076550U 146: file testGithub4508_2b.svg gave hash 1021344995U not the expected 4005636724U 146: file testGithub4538.svg gave hash 1030251935U not the expected 2797362550U 146: file testDarkMode.1.svg gave hash 1724545478U not the expected 4157562958U 146: file testMonochrome.1.svg gave hash 976079970U not the expected 482290994U 146: file testMonochrome.2.svg gave hash 2298962671U not the expected 2128285153U 146: file testAvalon.1.svg gave hash 447120226U not the expected 477303888U 146: file testCDK.1.svg gave hash 3760150813U not the expected 1764612361U 146: file testGithub4519_1.svg gave hash 3038145453U not the expected 736612670U 146: file testGithub4519_2.svg gave hash 2149902614U not the expected 171503813U 146: file testGithub4519_3.svg gave hash 2970193890U not the expected 3396792960U 146: file testGithub4519_4.svg gave hash 111372964U not the expected 3924693257U 136: *********************************************************** 136: Testing O3AAlign 136: --------------------------------- 136: testMMFFO3A 136: 136: --------------------------------- 136: testMMFFO3A with pre-computed dmat and MolHistogram 136: 136: --------------------------------- 136: testMMFFO3A with constraints 136: 136: --------------------------------- 136: testMMFFO3A with variable weight constraints followed by local-only optimization 136: 136: --------------------------------- 136: testCrippenO3A 136: 136: --------------------------------- 136: testCrippenO3A with pre-computed dmat and MolHistogram 136: 136: --------------------------------- 136: testCrippenO3A with constraints 136: 136: --------------------------------- 136: testCrippenO3A with variable weight constraints followed by local-only optimization 136: 136: --------------------------------- 136: testMMFFO3A multithreading 136: 136: generating reference data 146: file testBaseFontSize.1a.svg gave hash 4001693957U not the expected 1295117205U 146: file testBaseFontSize.1b.svg gave hash 4281598149U not the expected 3595811515U 146: ------------------------------------------------------------------------------- 146: changing baseFontSize 146: basics-small 146: ------------------------------------------------------------------------------- 146: ./Code/GraphMol/MolDraw2D/catch_tests.cpp:4086 146: ............................................................................... 146: 146: ./Code/GraphMol/MolDraw2D/catch_tests.cpp:4090: FAILED: 146: CHECK( drawer.fontSize() == Catch::Approx(14.0).margin(0.1) ) 146: with expansion: 146: 13.8691064545 == Approx( 14.0 ) 146: 146: file testBaseFontSize.2a.svg gave hash 4236623323U not the expected 2958687877U 146: file testBaseFontSize.2b.svg gave hash 3431978475U not the expected 1786972332U 146: file testFlexiCanvas.2.svg gave hash 3528076106U not the expected 665664909U 146: file testFlexiCanvas.2a.png gave hash 3809318030U not the expected 3217758043U 146: file testFlexiCanvas.2b.png gave hash 1941040420U not the expected 4070063910U 146: file testSemiFlexiCanvas.1c.svg gave hash 1887143568U not the expected 4178696811U 146: file testFlexiCanvas.3.svg gave hash 1498773600U not the expected 2819587550U 146: file testFlexiCanvas.6a.svg gave hash 3710806917U not the expected 3085867303U 146: file testFlexiCanvas.6b.svg gave hash 4179603074U not the expected 2819164642U 146: file testFlexiCanvas.6c.svg gave hash 3710806917U not the expected 3085867303U 146: file testFlexiCanvas.6d.svg gave hash 3710806917U not the expected 3085867303U 146: file testFlexiCanvas.7a.svg gave hash 128018593U not the expected 514767495U 146: file testFlexiCanvas.7b.svg gave hash 1791733144U not the expected 4275125955U 156/222 Test #166: trajectoryTest ......................... Passed 0.66 sec test 167 Start 167: substructLibraryTest 167: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest 167: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary 167: Test timeout computed to be: 1500 146: file testFlexiCanvas.7c.svg gave hash 128018593U not the expected 514767495U 146: file testFlexiCanvas.7d.svg gave hash 128018593U not the expected 514767495U 146: file testGithub4764.sz1.svg gave hash 2950365870U not the expected 3611125861U 146: file testGithub4764.sz2.svg gave hash 1059315367U not the expected 1936114454U 146: file testGithub4764.sz3.svg gave hash 157477816U not the expected 2712214121U 146: file testGithub4764.sz1.png gave hash 572630310U not the expected 98827714U 146: file testGithub4764.sz2.png gave hash 4058692402U not the expected 89252465U 167: [21:31:56] ------------------------------------- 167: [21:31:56] Test1 146: file testGithub4764.sz3.png gave hash 1519375648U not the expected 148503574U 146: file testDrawArc1.svg gave hash 693243455U not the expected 3279637525U 146: file testMetalWedges.svg gave hash 2458660191U not the expected 2896721486U 146: ------------------------------------------------------------------------------- 146: vary proportion of panel for legend 146: basics 146: ------------------------------------------------------------------------------- 146: ./Code/GraphMol/MolDraw2D/catch_tests.cpp:4632 146: ............................................................................... 146: 146: ./Code/GraphMol/MolDraw2D/catch_tests.cpp:4646: FAILED: 146: CHECK( text.find("getNumOnBits() 211: **** 211: 211: ... 211: ---------------------------------------------------------------------- 211: Ran 5 tests in 0.049s 211: 211: OK 201/222 Test #211: pyRanker ............................... Passed 0.53 sec test 212 Start 212: testChemicalFeatures 212: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures 212: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ChemicalFeatures 212: Test timeout computed to be: 1500 212: ----------------------------------------- 212: Test1 212: Done 202/222 Test #212: testChemicalFeatures ................... Passed 0.03 sec test 213 Start 213: pyFeatures 213: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap/testFeatures.py" 213: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap 213: Test timeout computed to be: 1500 207: ..... 207: ---------------------------------------------------------------------- 207: Ran 5 tests in 0.624s 207: 207: OK 203/222 Test #207: pyMatCalc .............................. Passed 1.31 sec test 214 Start 214: pythonTestDbCLI 214: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Projects/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/Projects" 214: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Projects 214: Test timeout computed to be: 1500 149: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 149: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 149: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 149: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 149: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 149: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 149: TOTAL Time elapsed 31.92 seconds 204/222 Test #149: testFMCS ............................... Passed 31.97 sec test 215 Start 215: pythonTestDirRoot 215: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit" 215: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit 215: Test timeout computed to be: 1500 205/222 Test #213: pyFeatures .............................***Exception: SegFault 0.34 sec test 216 Start 216: pythonTestDirML 216: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/ML/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/ML" 216: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit 216: Test timeout computed to be: 1500 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:21: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML import BuildComposite 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:83: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: refCompos = pickle.load(pklF) 215: ......................... 215: ---------------------------------------------------------------------- 215: Ran 25 tests in 0.888s 215: 215: OK 216: ...../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:198: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: refCompos = pickle.load(pklFile) 206/222 Test #215: pythonTestDirRoot ...................... Passed 1.28 sec test 217 Start 217: pythonTestDirDataStructs 217: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/DataStructs/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/DataStructs" 217: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit 217: Test timeout computed to be: 1500 216: . 216: ---------------------------------------------------------------------- 216: Ran 6 tests in 0.525s 216: 216: OK 210: ....... 210: ---------------------------------------------------------------------- 210: Ran 11 tests in 2.124s 210: 210: OK 207/222 Test #210: pySimDivPickers ........................ Passed 2.50 sec test 218 Start 218: pythonTestDirDbase 218: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase" 218: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit 218: Test timeout computed to be: 1500 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:20: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML import ScreenComposite 218: .. 218: ---------------------------------------------------------------------- 218: Ran 2 tests in 0.094s 218: 218: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:276: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: compos = pickle.load(pklF) 216: ../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:330: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: compos = pickle.load(pklF) 218: ........... 218: ---------------------------------------------------------------------- 218: Ran 11 tests in 0.052s 218: 218: OK 217: .................................. 217: ---------------------------------------------------------------------- 217: Ran 34 tests in 0.013s 217: 217: OK 216: .......... 216: ---------------------------------------------------------------------- 216: Ran 12 tests in 0.169s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:19: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML import AnalyzeComposite 218: . 218: ---------------------------------------------------------------------- 218: Ran 1 test in 0.006s 218: 218: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:31: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: c1 = pickle.load(pklF) 216: . 216: ---------------------------------------------------------------------- 216: Ran 1 test in 0.061s 216: 216: OK 217: ..... 217: ---------------------------------------------------------------------- 217: Ran 5 tests in 0.037s 217: 217: OK 214: FFFFFFFFFFFF 214: ====================================================================== 214: FAIL: test1Create (__main__.TestCase.test1Create) 214: ---------------------------------------------------------------------- 214: Traceback (most recent call last): 214: File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 22, in test1Create 214: self.assertFalse(res) 214: AssertionError: -11 is not false 214: 214: ====================================================================== 214: FAIL: test2_1SearchFPs (__main__.TestCase.test2_1SearchFPs) 214: ---------------------------------------------------------------------- 214: Traceback (most recent call last): 214: File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 74, in test2_1SearchFPs 214: self.assertTrue(os.path.exists('testData/bzr/Compounds.sqlt')) 214: AssertionError: False is not true 214: 214: ====================================================================== 214: FAIL: test2_2SearchAtomPairs (__main__.TestCase.test2_2SearchAtomPairs) 214: ---------------------------------------------------------------------- 214: Traceback (most recent call last): 214: File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 106, in test2_2SearchAtomPairs 214: self.assertTrue(os.path.exists('testData/bzr/Compounds.sqlt')) 214: AssertionError: False is not true 214: 214: ====================================================================== 214: FAIL: test2_3SearchTorsions (__main__.TestCase.test2_3SearchTorsions) 214: ---------------------------------------------------------------------- 214: Traceback (most recent call last): 214: File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 139, in test2_3SearchTorsions 214: self.assertTrue(os.path.exists('testData/bzr/Compounds.sqlt')) 214: AssertionError: False is not true 214: 214: ====================================================================== 214: FAIL: test2_4SearchProps (__main__.TestCase.test2_4SearchProps) 214: ---------------------------------------------------------------------- 214: Traceback (most recent call last): 214: File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 171, in test2_4SearchProps 214: self.assertTrue(os.path.exists('testData/bzr/Compounds.sqlt')) 214: AssertionError: False is not true 214: 214: ====================================================================== 214: FAIL: test2_5SearchSmarts (__main__.TestCase.test2_5SearchSmarts) 214: ---------------------------------------------------------------------- 214: Traceback (most recent call last): 214: File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 212, in test2_5SearchSmarts 214: self.assertFalse(res) 214: AssertionError: -11 is not false 214: 214: ====================================================================== 214: FAIL: test2_6SearchBoth (__main__.TestCase.test2_6SearchBoth) 214: ---------------------------------------------------------------------- 214: Traceback (most recent call last): 214: File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 276, in test2_6SearchBoth 214: self.assertFalse(res) 214: AssertionError: -11 is not false 214: 214: ====================================================================== 214: FAIL: test2_7SearchGobbi (__main__.TestCase.test2_7SearchGobbi) 214: ---------------------------------------------------------------------- 214: Traceback (most recent call last): 214: File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 300, in test2_7SearchGobbi 214: self.assertTrue(os.path.exists('testData/bzr/Compounds.sqlt')) 214: AssertionError: False is not true 214: 214: ====================================================================== 214: FAIL: test2_8SearchThresh (__main__.TestCase.test2_8SearchThresh) 214: ---------------------------------------------------------------------- 214: Traceback (most recent call last): 214: File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 335, in test2_8SearchThresh 214: self.assertTrue(os.path.exists('testData/bzr/Compounds.sqlt')) 214: AssertionError: False is not true 214: 214: ====================================================================== 214: FAIL: test4CreateOptions (__main__.TestCase.test4CreateOptions) 214: ---------------------------------------------------------------------- 214: Traceback (most recent call last): 214: File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 372, in test4CreateOptions 214: self.assertFalse(res) 214: AssertionError: -11 is not false 214: 214: ====================================================================== 214: FAIL: test5TestBackwardsCompat (__main__.TestCase.test5TestBackwardsCompat) 214: ---------------------------------------------------------------------- 214: Traceback (most recent call last): 214: File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 495, in test5TestBackwardsCompat 214: self.assertFalse(res) 214: AssertionError: -11 is not false 214: 214: ====================================================================== 214: FAIL: test6Update (__main__.TestCase.test6Update) 214: ---------------------------------------------------------------------- 214: Traceback (most recent call last): 214: File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 531, in test6Update 214: self.assertFalse(res) 214: AssertionError: -11 is not false 214: 214: ---------------------------------------------------------------------- 214: Ran 12 tests in 2.424s 214: 214: FAILED (failures=12) 214: !!! TEST FAILURE: python TestDbCLI.py {'dir': 'DbCLI'} 218: ............... 218: ---------------------------------------------------------------------- 218: Ran 15 tests in 0.160s 218: 218: OK 208/222 Test #214: pythonTestDbCLI ........................***Failed 2.96 sec FFFFFFFFFFFF ====================================================================== FAIL: test1Create (__main__.TestCase.test1Create) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 22, in test1Create self.assertFalse(res) AssertionError: -11 is not false ====================================================================== FAIL: test2_1SearchFPs (__main__.TestCase.test2_1SearchFPs) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 74, in test2_1SearchFPs self.assertTrue(os.path.exists('testData/bzr/Compounds.sqlt')) AssertionError: False is not true ====================================================================== FAIL: test2_2SearchAtomPairs (__main__.TestCase.test2_2SearchAtomPairs) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 106, in test2_2SearchAtomPairs self.assertTrue(os.path.exists('testData/bzr/Compounds.sqlt')) AssertionError: False is not true ====================================================================== FAIL: test2_3SearchTorsions (__main__.TestCase.test2_3SearchTorsions) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 139, in test2_3SearchTorsions self.assertTrue(os.path.exists('testData/bzr/Compounds.sqlt')) AssertionError: False is not true ====================================================================== FAIL: test2_4SearchProps (__main__.TestCase.test2_4SearchProps) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 171, in test2_4SearchProps self.assertTrue(os.path.exists('testData/bzr/Compounds.sqlt')) AssertionError: False is not true ====================================================================== FAIL: test2_5SearchSmarts (__main__.TestCase.test2_5SearchSmarts) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 212, in test2_5SearchSmarts self.assertFalse(res) AssertionError: -11 is not false ====================================================================== FAIL: test2_6SearchBoth (__main__.TestCase.test2_6SearchBoth) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 276, in test2_6SearchBoth self.assertFalse(res) AssertionError: -11 is not false ====================================================================== FAIL: test2_7SearchGobbi (__main__.TestCase.test2_7SearchGobbi) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 300, in test2_7SearchGobbi self.assertTrue(os.path.exists('testData/bzr/Compounds.sqlt')) AssertionError: False is not true ====================================================================== FAIL: test2_8SearchThresh (__main__.TestCase.test2_8SearchThresh) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 335, in test2_8SearchThresh self.assertTrue(os.path.exists('testData/bzr/Compounds.sqlt')) AssertionError: False is not true ====================================================================== FAIL: test4CreateOptions (__main__.TestCase.test4CreateOptions) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 372, in test4CreateOptions self.assertFalse(res) AssertionError: -11 is not false ====================================================================== FAIL: test5TestBackwardsCompat (__main__.TestCase.test5TestBackwardsCompat) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 495, in test5TestBackwardsCompat self.assertFalse(res) AssertionError: -11 is not false ====================================================================== FAIL: test6Update (__main__.TestCase.test6Update) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/Projects/DbCLI/TestDbCLI.py", line 531, in test6Update self.assertFalse(res) AssertionError: -11 is not false ---------------------------------------------------------------------- Ran 12 tests in 2.424s FAILED (failures=12) !!! TEST FAILURE: python TestDbCLI.py {'dir': 'DbCLI'} test 219 Start 219: pythonTestDirSimDivFilters 219: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/SimDivFilters/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/SimDivFilters" 219: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit 219: Test timeout computed to be: 1500 217: ....... 217: ---------------------------------------------------------------------- 217: Ran 7 tests in 0.002s 217: 217: OK 217: !!! TEST FAILURE: python UnitTestDocTests.py {} 209/222 Test #217: pythonTestDirDataStructs ...............***Failed 1.87 sec .................................. ---------------------------------------------------------------------- Ran 34 tests in 0.013s OK ..... ---------------------------------------------------------------------- Ran 5 tests in 0.037s OK ....... ---------------------------------------------------------------------- Ran 7 tests in 0.002s OK !!! TEST FAILURE: python UnitTestDocTests.py {} test 220 Start 220: pythonTestDirVLib 220: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/VLib/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/VLib" 220: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit 220: Test timeout computed to be: 1500 218: ...... 218: ---------------------------------------------------------------------- 218: Ran 6 tests in 0.007s 218: 218: OK 216: ... 216: ---------------------------------------------------------------------- 216: Ran 3 tests in 0.002s 216: 216: OK 210/222 Test #218: pythonTestDirDbase ..................... Passed 1.78 sec test 221 Start 221: pythonTestSping 221: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/sping" 221: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit 221: Test timeout computed to be: 1500 219: !!! TEST FAILURE: python SimilarityPickers.py {} 211/222 Test #219: pythonTestDirSimDivFilters .............***Failed 0.46 sec !!! TEST FAILURE: python SimilarityPickers.py {} test 222 Start 222: pythonTestDirChem 222: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/Chem" "--buildType" "None" 222: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit/Chem 222: Test timeout computed to be: 1500 220: ............. 220: ---------------------------------------------------------------------- 220: Ran 13 tests in 0.016s 220: 220: OK 212/222 Test #221: pythonTestSping ........................***Exception: SegFault 0.36 sec 213/222 Test #222: pythonTestDirChem ......................***Exception: SegFault 0.29 sec 216: ........ 216: ---------------------------------------------------------------------- 216: Ran 8 tests in 0.001s 216: 216: OK 220: !!! TEST FAILURE: python UnitTestNodeLib.py {} 220: !!! TEST FAILURE: python test_list.py {'dir': 'NodeLib'} 214/222 Test #220: pythonTestDirVLib ......................***Failed 0.80 sec ............. ---------------------------------------------------------------------- Ran 13 tests in 0.016s OK !!! TEST FAILURE: python UnitTestNodeLib.py {} !!! TEST FAILURE: python test_list.py {'dir': 'NodeLib'} 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.Composite import Composite 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree.DecTree import DecTreeNode as Node 216: .... 216: ---------------------------------------------------------------------- 216: Ran 4 tests in 0.211s 216: 216: OK 216: ..... 216: ---------------------------------------------------------------------- 216: Ran 5 tests in 0.003s 216: 216: OK 216: ......... 216: ---------------------------------------------------------------------- 216: Ran 9 tests in 0.005s 216: 216: OK 216: ............ 216: ---------------------------------------------------------------------- 216: Ran 12 tests in 0.003s 216: 216: OK 216: ..... 216: ---------------------------------------------------------------------- 216: Ran 5 tests in 0.100s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestTreeUtils.py:8: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree import TreeUtils 216: . 216: ---------------------------------------------------------------------- 216: Ran 1 test in 0.000s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestTree.py:13: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree import Tree 216: ...... 216: ---------------------------------------------------------------------- 216: Ran 6 tests in 0.002s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestXVal.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree import CrossValidate, randomtest 216: .... 216: ---------------------------------------------------------------------- 216: Ran 4 tests in 0.251s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestID3.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree import ID3 216: ...... 216: ---------------------------------------------------------------------- 216: Ran 6 tests in 0.022s 216: 216: OK 29: [21:32:32] Finished 29: [21:32:32] ------------------------------------- 29: [21:32:32] Test github1843: RWMol.clear() should not destroy ring pointer. 29: [21:32:32] Finished 215/222 Test #29: graphmolTest1 .......................... Passed 62.39 sec 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestPrune.py:9: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree import ID3, CrossValidate, PruneTree 216: .. 216: ---------------------------------------------------------------------- 216: Ran 2 tests in 0.158s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestQuantTree.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree import BuildQuantTree 216: .......... 216: ---------------------------------------------------------------------- 216: Ran 10 tests in 0.013s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestSigTree.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree.BuildSigTree import BuildSigTree, _GenerateRandomEnsemble 136: --------------------------------- 136: test O3A multithreading bug 136: 136: --------------------------------- 136: testCrippenO3A multithreading 136: 136: generating reference data 216: ..... 216: ---------------------------------------------------------------------- 216: Ran 5 tests in 0.210s 216: 216: OK 216: .. 216: ---------------------------------------------------------------------- 216: Ran 2 tests in 0.007s 216: 216: OK 216: ... 216: ---------------------------------------------------------------------- 216: Ran 3 tests in 0.019s 216: 216: OK 136: processing 136: launch :0 136: launch :1 136: launch :2 136: launch :3 216: !!! TEST FAILURE: python UnitTestMolDescriptors.py {} 216: ... 216: ---------------------------------------------------------------------- 216: Ran 3 tests in 0.572s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/KNN/UnitTestKNN.py:11: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.KNN import (CrossValidate, DistFunctions, KNNModel, 216: ...... 216: ---------------------------------------------------------------------- 216: Ran 6 tests in 0.499s 216: 216: OK 216: !!! TEST FAILURE: python UnitTestPackage.py {} 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/NaiveBayes/UnitTestNB.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.NaiveBayes import CrossValidate 216: .... 216: ---------------------------------------------------------------------- 216: Ran 4 tests in 0.015s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Neural/UnitTestTrainer.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.Neural import Network, Trainers 216: ..... 216: ---------------------------------------------------------------------- 216: Ran 5 tests in 3.342s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Neural/UnitTestOther.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.Neural.ActFuncs import Sigmoid, TanH 216: .... 216: ---------------------------------------------------------------------- 216: Ran 4 tests in 0.002s 216: 216: OK 216: .... 216: ---------------------------------------------------------------------- 216: Ran 4 tests in 0.001s 216: 216: OK 216: .... 216: ---------------------------------------------------------------------- 216: Ran 4 tests in 0.005s 216: 216: OK 216: !!! TEST FAILURE: python test_list.py {'dir': 'Descriptors'} 216: !!! TEST FAILURE: python test_list.py {'dir': 'ModelPackage'} 216/222 Test #216: pythonTestDirML ........................***Failed 18.54 sec /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:21: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML import BuildComposite /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:83: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release refCompos = pickle.load(pklF) ...../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:198: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release refCompos = pickle.load(pklFile) . ---------------------------------------------------------------------- Ran 6 tests in 0.525s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:20: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML import ScreenComposite /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:276: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release compos = pickle.load(pklF) ../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:330: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release compos = pickle.load(pklF) .......... ---------------------------------------------------------------------- Ran 12 tests in 0.169s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:19: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML import AnalyzeComposite /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:31: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release c1 = pickle.load(pklF) . ---------------------------------------------------------------------- Ran 1 test in 0.061s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.002s OK ........ ---------------------------------------------------------------------- Ran 8 tests in 0.001s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.Composite import Composite /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.DecTree.DecTree import DecTreeNode as Node .... ---------------------------------------------------------------------- Ran 4 tests in 0.211s OK ..... ---------------------------------------------------------------------- Ran 5 tests in 0.003s OK ......... ---------------------------------------------------------------------- Ran 9 tests in 0.005s OK ............ ---------------------------------------------------------------------- Ran 12 tests in 0.003s OK ..... ---------------------------------------------------------------------- Ran 5 tests in 0.100s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestTreeUtils.py:8: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.DecTree import TreeUtils . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestTree.py:13: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.DecTree import Tree ...... ---------------------------------------------------------------------- Ran 6 tests in 0.002s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestXVal.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.DecTree import CrossValidate, randomtest .... ---------------------------------------------------------------------- Ran 4 tests in 0.251s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestID3.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.DecTree import ID3 ...... ---------------------------------------------------------------------- Ran 6 tests in 0.022s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestPrune.py:9: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.DecTree import ID3, CrossValidate, PruneTree .. ---------------------------------------------------------------------- Ran 2 tests in 0.158s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestQuantTree.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.DecTree import BuildQuantTree .......... ---------------------------------------------------------------------- Ran 10 tests in 0.013s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestSigTree.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.DecTree.BuildSigTree import BuildSigTree, _GenerateRandomEnsemble ..... ---------------------------------------------------------------------- Ran 5 tests in 0.210s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.007s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.019s OK !!! TEST FAILURE: python UnitTestMolDescriptors.py {} ... ---------------------------------------------------------------------- Ran 3 tests in 0.572s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/KNN/UnitTestKNN.py:11: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.KNN import (CrossValidate, DistFunctions, KNNModel, ...... ---------------------------------------------------------------------- Ran 6 tests in 0.499s OK !!! TEST FAILURE: python UnitTestPackage.py {} /build/reproducible-path/rdkit-202309.3/rdkit/ML/NaiveBayes/UnitTestNB.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.NaiveBayes import CrossValidate .... ---------------------------------------------------------------------- Ran 4 tests in 0.015s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/Neural/UnitTestTrainer.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.Neural import Network, Trainers ..... ---------------------------------------------------------------------- Ran 5 tests in 3.342s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/Neural/UnitTestOther.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.Neural.ActFuncs import Sigmoid, TanH .... ---------------------------------------------------------------------- Ran 4 tests in 0.002s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.001s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.005s OK !!! TEST FAILURE: python test_list.py {'dir': 'Descriptors'} !!! TEST FAILURE: python test_list.py {'dir': 'ModelPackage'} 136: --------------------------------- 136: test getO3AForProbeConfs 136: 136: *********************************************************** 217/222 Test #136: testO3AAlign ........................... Passed 68.53 sec 133: [21:33:04] UFFTYPER: Unrecognized atom type: S_6+6 (0) 133: [21:33:04] UFFTYPER: Warning: hybridization set to SP3 for atom 0 133: [21:33:04] UFFTYPER: Unrecognized charge state for atom: 0 133: =============================================================================== 133: All tests passed (448 assertions in 10 test cases) 133: 218/222 Test #133: distGeomHelpersCatch ................... Passed 81.56 sec 157: =============================================================================== 157: All tests passed (93 assertions in 5 test cases) 157: 219/222 Test #157: testRascalCluster ...................... Passed 76.73 sec 5: [21:33:18] Finished: testMultipleTimes() 5: [21:33:18] 5: ----------------------------------------- 220/222 Test #5: testConcurrentQueue .................... Passed 109.03 sec 132: [21:33:43] done 132: CNC[C@H]1CC[C@H](C[NH3+])CC1 132: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 132: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 132: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 132: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 156: =============================================================================== 156: All tests passed (2552 assertions in 23 test cases) 156: 221/222 Test #156: testRascalMCES ......................... Passed 122.92 sec 132: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O 132: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 132: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 132: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 132: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC 132: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O 132: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 132: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 132: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 132: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 132: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 132: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O 132: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O 132: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 132: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 132: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 132: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 132: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 132: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 132: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 132: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 132: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 132: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 132: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] 132: [21:34:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [21:34:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [21:34:35] Molecule does not have explicit Hs. Consider calling AddHs() 222/222 Test #132: testDistGeomHelpers .................... Passed 171.46 sec 73% tests passed, 61 tests failed out of 222 Total Test time (real) = 186.23 sec The following tests FAILED: 2 - pyCoordGen (SEGFAULT) 20 - testConrec (Failed) 26 - pyForceFieldConstraints (SEGFAULT) 61 - pyDepictor (SEGFAULT) 62 - testMrvToMol (Subprocess aborted) 85 - pyChemReactions (SEGFAULT) 86 - pyChemReactionEnumerations (SEGFAULT) 87 - pyChemReactionSanitize (SEGFAULT) 91 - pyTautomerQuery (SEGFAULT) 96 - pyFilterCatalog (SEGFAULT) 98 - pyFragCatalog (SEGFAULT) 114 - pyMolDescriptors (SEGFAULT) 115 - pyMolDescriptors3D (SEGFAULT) 119 - fpTestCatch (Failed) 121 - pyTestGenerator (SEGFAULT) 122 - pyTestMHFP (SEGFAULT) 124 - pyPartialCharges (SEGFAULT) 126 - pyMolTransforms (SEGFAULT) 131 - pyForceFieldHelpers (SEGFAULT) 134 - pyDistGeomHelpers (SEGFAULT) 138 - pyMolAlign (SEGFAULT) 140 - pyChemicalFeatures (SEGFAULT) 142 - pyShapeHelpers (SEGFAULT) 144 - pyMolCatalog (SEGFAULT) 145 - moldraw2DTest1 (Subprocess aborted) 146 - moldraw2DTestCatch (Failed) 148 - pyMolDraw2D (SEGFAULT) 150 - pyFMCS (SEGFAULT) 153 - pyMolHash (SEGFAULT) 155 - pyMMPA (SEGFAULT) 158 - pyMolDraw2D (SEGFAULT) 160 - pyCIPLabelsWrapTest (SEGFAULT) 161 - pyCIPLabelsValidation (SEGFAULT) 163 - pyDeprotect (SEGFAULT) 165 - pyReducedGraphs (SEGFAULT) 169 - pySubstructLibrary (SEGFAULT) 173 - pyRGroupDecomposition (SEGFAULT) 176 - pyMolInterchange (SEGFAULT) 178 - pySLNParse (SEGFAULT) 179 - pyGraphMolWrap (SEGFAULT) 180 - pyTestConformerWrap (SEGFAULT) 181 - pyTestTrajectory (SEGFAULT) 182 - pyTestSGroups (SEGFAULT) 183 - pyTestThreads (SEGFAULT) 184 - pyTestMultithreadedMolSupplier (SEGFAULT) 185 - pyTestPropertyLists (SEGFAULT) 186 - pyCDXMLTest (SEGFAULT) 195 - pyMolStandardize (SEGFAULT) 197 - pyScaffoldNetwork (SEGFAULT) 198 - pyScaffoldNetworkPickling (SEGFAULT) 200 - pyMolEnumerator (SEGFAULT) 202 - pyAbbreviations (SEGFAULT) 204 - pyGeneralizedSubstruct (SEGFAULT) 213 - pyFeatures (SEGFAULT) 214 - pythonTestDbCLI (Failed) 216 - pythonTestDirML (Failed) 217 - pythonTestDirDataStructs (Failed) 219 - pythonTestDirSimDivFilters (Failed) 220 - pythonTestDirVLib (Failed) 221 - pythonTestSping (SEGFAULT) 222 - pythonTestDirChem (SEGFAULT) Errors while running CTest make[2]: *** [Makefile:94: test] Error 8 make[2]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' dh_auto_test: error: cd obj-i686-linux-gnu && make -j11 test ARGS\+=--verbose ARGS\+=-j11 returned exit code 2 make[1]: [debian/rules:133: override_dh_auto_test] Error 25 (ignored) make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_installdirs -O--buildsystem=cmake debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_auto_install cd obj-i686-linux-gnu && make -j11 install DESTDIR=/build/reproducible-path/rdkit-202309.3/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202309.3 -B/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Cluster -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Cluster/Resemblance.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Cluster/__pycache__ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Cluster/ClusterVis.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Cluster/Butina.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Cluster/Murtagh.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Cluster/Clusters.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Cluster/murtagh_test.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Cluster/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Cluster/ClusterUtils.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Cluster/Standardize.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/InfoTheory -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/InfoTheory/entropy.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/InfoTheory/BitClusterer.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/InfoTheory/__pycache__ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/InfoTheory/BitRank.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/InfoTheory/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/files.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/ModelPackage -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/ModelPackage/__pycache__ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/ModelPackage/PackageUtils.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/ModelPackage/Packager.py -- Installing: 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Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/patches -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/README -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/examples -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/examples/formatted-strings.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/utils.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/pid.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/ReportLab -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/ReportLab/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/ReportLab/pidReportLab.py -- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitForceField.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/Contrib.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/ForceField.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleBend.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/BondStretch.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/Contribs.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/DistanceConstraint.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleConstraint.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionConstraint.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/PositionConstraint.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/Nonbonded.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/Params.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/Inversion.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionAngle.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleBend.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/BondStretch.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/StretchBend.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/OopBend.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionAngle.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/Nonbonded.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/Contribs.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/DistanceConstraint.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleConstraint.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionConstraint.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/PositionConstraint.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/Params.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ForceField/rdForceField.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDistGeometry.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDistGeometry.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDistGeometry.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DistGeom/BoundsMatrix.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DistGeom/ChiralSet.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DistGeom/ChiralViolationContrib.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DistGeom/DistGeomUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DistGeom/DistViolationContrib.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DistGeom/FourthDimContrib.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DistGeom/TriangleSmooth.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/DistanceGeometry/DistGeom.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitCatalogs.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitCatalogs.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitCatalogs.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Catalogs/CatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Catalogs/Catalog.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Catalogs/CatalogParams.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGraphMol.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGraphMol.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGraphMol.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Atom.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/atomic_data.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/AtomIterators.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Bond.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/BondIterators.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Canon.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Chirality.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Conformer.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/details.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/GraphMol.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolOps.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolPickler.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/PeriodicTable.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/QueryAtom.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/QueryBond.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/QueryOps.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RDKitBase.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RDKitQueries.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Resonance.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RingInfo.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Rings.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ROMol.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RWMol.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SanitException.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SubstanceGroup.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/StereoGroup.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MonomerInfo.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/new_canon.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolBundle.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSmilesParse.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSmilesParse.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSmilesParse.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/primes.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmartsWrite.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParse.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParseOps.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesWrite.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDepictor.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDepictor.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDepictor.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Depictor/DepictUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Depictor/EmbeddedFrag.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Depictor/RDDepictor.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdDepictor.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMarvinParser.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMarvinParser.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMarvinParser.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MarvinParser/MarvinParser.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFileParsers.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFileParsers.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFileParsers.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/CDXMLParser.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParsers.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParserUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolFileStereochem.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolSupplier.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolWriters.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceParsers.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceWriters.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/GeneralFileReader.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSDMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/PNGParser.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSubstructMatch.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGenericGroups.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGenericGroups.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGenericGroups.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/GenericGroups/GenericGroups.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemReactions.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemReactions.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemReactions.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Reaction.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionParser.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionPickler.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionFingerprints.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionRunner.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/PreprocessRxn.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/SanitizeRxn.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/Enumerate.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateBase.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/CartesianProduct.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSample.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdChemReactions.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemTransforms.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemTransforms.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemTransforms.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/ChemTransforms.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/MolFragmenter.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitTautomerQuery.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/TautomerQuery/TautomerQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdTautomerQuery.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSubgraphs.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSubgraphs.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSubgraphs.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/Subgraphs.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/SubgraphUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFilterCatalog.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalog.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatcherBase.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatchers.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdfiltercatalog.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFragCatalog.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFragCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFragCatalog.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatGenerator.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatParams.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragFPGenerator.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdfragcatalog.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDescriptors.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDescriptors.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDescriptors.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Crippen.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/BCUT.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Lipinski.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolDescriptors.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolSurf.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/ConnectivityDescriptors.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MQN.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/RegisterDescriptor.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Property.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AUTOCORR2D.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Data3Ddescriptors.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolData3Ddescriptors.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/USRDescriptor.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AtomFeat.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/OxidationNumbers.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolDescriptors3D.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/EEM.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/PBF.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/PMI.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AUTOCORR3D.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/RDF.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MORSE.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/GETAWAY.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/WHIM.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/CoulombMat.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdMolDescriptors.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFingerprints.so.1.2023.09.3 -- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/AtomPairGenerator.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MorganGenerator.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/RDKitFPGenerator.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/TopologicalTorsionGenerator.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/FingerprintUtil.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdFingerprintGenerator.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdMHFPFingerprint.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitPartialCharges.so.1.2023.09.3 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolTransforms/MolTransforms.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdMolTransforms.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/FFConvenience.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/Builder.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/UFF.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/Builder.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/MMFF.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdForceFieldHelpers.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/Embedder.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdDistGeom.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolAlign.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolAlign.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolAlign.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitO3AAlign.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitO3AAlign.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitO3AAlign.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/AlignMolecules.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/O3AAlignMolecules.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdMolAlign.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/FeatureParser.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdMolChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitShapeHelpers.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeEncoder.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdShapeHelpers.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolCatalog.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolCatalog.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalog.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdMolCatalog.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2D.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2Dwx.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DJS.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DHelpers.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolDraw2D.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DCairo.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Draw/rdMolDraw2D.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFMCS.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFMCS.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFMCS.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FMCS/FMCS.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FMCS/Graph.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdFMCS.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolHash.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolHash.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolHash.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolHash/MolHash.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolHash/nmmolhash.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdMolHash.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMMPA.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMMPA.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMMPA.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MMPA/MMPA.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdMMPA.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRascalMCES.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRascalMCES.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRascalMCES.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalMCES.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalOptions.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalClusterOptions.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalResult.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdRascalMCES.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitCIPLabeler.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/CIPLabeler/CIPLabeler.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/CIPLabeler/TooManyNodesException.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdCIPLabeler.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDeprotect.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDeprotect.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDeprotect.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Deprotect/Deprotect.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdDeprotect.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitReducedGraphs.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ReducedGraphs/ReducedGraphs.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdReducedGraphs.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitTrajectory.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitTrajectory.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitTrajectory.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Snapshot.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Trajectory.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSubstructLibrary.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrary.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/PatternFactory.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdSubstructLibrary.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecomp.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecompParams.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdRGroupDecomposition.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolInterchange.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolInterchange.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolInterchange.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/MolInterchange.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/details.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdMolInterchange.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSLNParse.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSLNParse.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSLNParse.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNAttribs.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNParse.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNParseOps.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdSLNParse.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdchem.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdmolops.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdqueries.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdmolfiles.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdtrajectory.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolStandardize.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolStandardize.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolStandardize.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/MolStandardize.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Metal.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Normalize.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Validate.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Charge.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Tautomer.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Fragment.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolStandardize/rdMolStandardize.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolEnumerator.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolEnumerator.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolEnumerator.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolEnumerator/MolEnumerator.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolEnumerator/LinkNode.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdMolEnumerator.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitAbbreviations.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitAbbreviations.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitAbbreviations.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Abbreviations/Abbreviations.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdAbbreviations.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGeneralizedSubstruct.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGeneralizedSubstruct.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/GeneralizedSubstruct/XQMol.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdGeneralizedSubstruct.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/AndQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/EqualityQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/GreaterEqualQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/GreaterQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/LessEqualQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/LessQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/NullQueryAlgebra.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/OrQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/Query.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/QueryObjects.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/RangeQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/SetQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/XOrQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Features/Feature.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricFuncs.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricMatrixCalc.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/DataManip/Metric/rdMetricMatrixCalc.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSimDivPickers.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/SimDivPickers/DistPicker.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/SimDivPickers/LeaderPicker.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/SimDivPickers/HierarchicalClusterPicker.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/SimDivPickers/MaxMinPicker.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/SimDivFilters/rdSimDivPickers.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKithc.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKithc.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKithc.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Cluster/Clustering.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitInfoTheory.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitInfoTheory.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitInfoTheory.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/InfoTheory/rdInfoTheory.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Data/cQuantize.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ChemicalFeatures/ChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ChemicalFeatures/FreeChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/rdChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/RDPaths.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets.cmake -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets-none.cmake -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/cmake/rdkit/rdkit-config.cmake -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/cmake/rdkit/rdkit-config-version.cmake make[2]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' mkdir -p /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3 mv /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3/dist-packages rm -f -rf /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11 ln -sf /usr/share/fonts/truetype/freefont/FreeSans.ttf /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/FreeSans.ttf dh_install -ppython3-rdkit /usr/lib/python3 rm -f -rf /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/docs/ rm -f -rf /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/__pycache__ dh_numpy3 dh_install mkdir -p /build/reproducible-path/rdkit-202309.3/debian/rdkit-doc/usr/share/doc/rdkit/ # cp /build/reproducible-path/rdkit-202309.3/Docs/Book/_build/latex/RDKit.pdf /build/reproducible-path/rdkit-202309.3/debian/rdkit-doc/usr/share/doc/rdkit/ cp -a /build/reproducible-path/rdkit-202309.3/Docs/Book/_build/html /build/reproducible-path/rdkit-202309.3/debian/rdkit-doc/usr/share/doc/rdkit/ pg_buildext install /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit build-%v postgresql-%v-rdkit ### PostgreSQL 16 install ### make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/build-16' /bin/mkdir -p '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib' /bin/mkdir -p '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/share/postgresql/16/extension' /bin/mkdir -p '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/share/postgresql/16/extension' /usr/bin/install -c -m 755 rdkit.so '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/rdkit.so' /usr/bin/install -c -m 644 /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit.control '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/share/postgresql/16/extension/' /usr/bin/install -c -m 644 rdkit--4.4.0.sql '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/share/postgresql/16/extension/' /bin/mkdir -p '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/bitcode/rdkit' /bin/mkdir -p '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/bitcode'/rdkit/ /usr/bin/install -c -m 644 rdkit_io.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 mol_op.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_op.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 sfp_op.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 rxn_op.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 rdkit_gist.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_gist.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_gin.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 low_gist.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 guc.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 cache.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 adapter.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bitstring.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/bitcode'/rdkit/./ cd '/build/reproducible-path/rdkit-202309.3/debian/postgresql-16-rdkit/usr/lib/postgresql/16/lib/bitcode' && /usr/lib/llvm-16/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-202309.3/build-16' ### End 16 install ### ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202309.3/debian/rdkit-doc/usr/share/doc/rdkit//html/cppapi/jquery.js ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202309.3/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/jquery.js ln -sf /usr/share/javascript/underscore/underscore.js /build/reproducible-path/rdkit-202309.3/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/underscore.js make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' dh_installdocs -O--buildsystem=cmake debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_installchangelogs ReleaseNotes.md make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_python3 -ppython3-rdkit I: dh_python3 fs:418: renaming rdBase.so to rdBase.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming Clustering.so to Clustering.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdInfoTheory.so to rdInfoTheory.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming cQuantize.so to cQuantize.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdGeometry.so to rdGeometry.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdAlignment.so to rdAlignment.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdAbbreviations.so to rdAbbreviations.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdCIPLabeler.so to rdCIPLabeler.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdChemReactions.so to rdChemReactions.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdChemicalFeatures.so to rdChemicalFeatures.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdCoordGen.so to rdCoordGen.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdDepictor.so to rdDepictor.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdDeprotect.so to rdDeprotect.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdDistGeom.so to rdDistGeom.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdFMCS.so to rdFMCS.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdFingerprintGenerator.so to rdFingerprintGenerator.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdForceFieldHelpers.so to rdForceFieldHelpers.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdGeneralizedSubstruct.so to rdGeneralizedSubstruct.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdMHFPFingerprint.so to rdMHFPFingerprint.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdMMPA.so to rdMMPA.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdMolAlign.so to rdMolAlign.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdMolCatalog.so to rdMolCatalog.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdMolChemicalFeatures.so to rdMolChemicalFeatures.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdMolDescriptors.so to rdMolDescriptors.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdMolEnumerator.so to rdMolEnumerator.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdMolHash.so to rdMolHash.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdMolInterchange.so to rdMolInterchange.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdMolTransforms.so to rdMolTransforms.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdPartialCharges.so to rdPartialCharges.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdRGroupDecomposition.so to rdRGroupDecomposition.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdRascalMCES.so to rdRascalMCES.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdReducedGraphs.so to rdReducedGraphs.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdSLNParse.so to rdSLNParse.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdShapeHelpers.so to rdShapeHelpers.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdSubstructLibrary.so to rdSubstructLibrary.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdTautomerQuery.so to rdTautomerQuery.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdchem.so to rdchem.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdfiltercatalog.so to rdfiltercatalog.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdfragcatalog.so to rdfragcatalog.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdmolfiles.so to rdmolfiles.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdmolops.so to rdmolops.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdqueries.so to rdqueries.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdtrajectory.so to rdtrajectory.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdMolStandardize.so to rdMolStandardize.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming DistGeom.so to DistGeom.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming cDataStructs.so to cDataStructs.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming rdForceField.so to rdForceField.cpython-311-i386-linux-gnu.so dh_numpy3 -ppython3-rdkit make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' dh_installsystemduser -O--buildsystem=cmake dh_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake dh_link -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake dh_fixperms -O--buildsystem=cmake debian/rules override_dh_missing make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_missing --list-missing 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/Cookbook.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/GettingStartedInC++.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/GettingStartedInPython.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/Install.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/Makefile exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/Overview.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/RDKit_Book.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/api-docs.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/conf.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/5ht3ligs.sdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/AmideBond.rxn exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/MinimalFeatures.fdef exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/README.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf.gz exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/bzr.sdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/bzr.smi exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/cdk2.sdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/chiral.mol exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/input.mol exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/invalid.mol exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/s1p_chembldoc89753.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/solubility.test.sdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/solubility.train.sdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/test_multi_colours.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/exts/extapi.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/Cc1ccccc1.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molA.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molB.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molC.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molD.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molE.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molF.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molG.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_0_im0.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_0_im1.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_0_im2.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_13_im0.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_13_im1.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_17_im0.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_17_im1.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_19_im0.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_1_im0.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_1_im1.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_1_im2.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_1_im3.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_20_im0.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_20_im1.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_21_im0.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_21_im1.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_21_im2.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_21_im3.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_21_im4.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_21_im5.png exists in debian/tmp but is not 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usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-MutipleCores.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-StereoChemTest.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/compounds.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/RD.css exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/README exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/FeatFinderCLI.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/PythonFormat.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/README.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/create_deb_packages.sh exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/test.sh exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/license.txt exists in debian/tmp but is not installed to anywhere The following debhelper tools have reported what they installed (with files per package) * dh_install: librdkit-dev (60), librdkit1t64 (116), postgresql-16-rdkit (0), python3-rdkit (1), rdkit-data (3), rdkit-doc (0) * dh_installdocs: librdkit-dev (0), librdkit1t64 (0), postgresql-16-rdkit (0), python3-rdkit (0), rdkit-data (0), rdkit-doc (0) If the missing files are installed by another tool, please file a bug against it. When filing the report, if the tool is not part of debhelper itself, please reference the "Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+). (in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.md.gz) Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built If the omission is intentional or no other helper can take care of this consider adding the paths to debian/not-installed. make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' dh_dwz -a -O--buildsystem=cmake dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake 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 rdkit-data: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-16-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dpkg-gencontrol: warning: package rdkit-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-16-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202309.3-4~exp1_i386.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202309.3-4~exp1_all.deb'. dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202309.3-4~exp1_i386.deb'. dpkg-deb: building package 'postgresql-16-rdkit' in '../postgresql-16-rdkit_202309.3-4~exp1_i386.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202309.3-4~exp1_i386.deb'. dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202309.3-4~exp1_i386.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202309.3-4~exp1_all.deb'. dpkg-deb: building package 'postgresql-16-rdkit-dbgsym' in '../postgresql-16-rdkit-dbgsym_202309.3-4~exp1_i386.deb'. dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202309.3-4~exp1_i386.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202309.3-4~exp1_i386.buildinfo dpkg-genchanges --build=binary -O../rdkit_202309.3-4~exp1_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: not including original source code in upload I: copying local configuration 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/8420 and its subdirectories I: Current time: Fri Apr 26 21:38:03 -12 2024 I: pbuilder-time-stamp: 1714210683 Sat Apr 27 09:38:06 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Sat Apr 27 09:38:06 UTC 2024 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Sat Apr 27 10:14:45 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. Sat Apr 27 10:14:46 UTC 2024 I: rdkit_202309.3-4~exp1_i386.changes: Format: 1.8 Date: Fri, 26 Apr 2024 09:28:39 +0300 Source: rdkit Binary: librdkit-dev librdkit1t64 librdkit1t64-dbgsym postgresql-16-rdkit postgresql-16-rdkit-dbgsym python3-rdkit python3-rdkit-dbgsym rdkit-data rdkit-doc Architecture: i386 all Version: 202309.3-4~exp1 Distribution: experimental Urgency: medium Maintainer: Debichem Team Changed-By: Andrius Merkys Description: librdkit-dev - Collection of cheminformatics and machine-learning software (deve librdkit1t64 - Collection of cheminformatics and machine-learning software (shar postgresql-16-rdkit - Cheminformatics and machine-learning software (PostgreSQL Cartrid python3-rdkit - Collection of cheminformatics and machine-learning software rdkit-data - Collection of cheminformatics and machine-learning software (data rdkit-doc - Collection of cheminformatics and machine-learning software (docu Changes: rdkit (202309.3-4~exp1) experimental; urgency=medium . * Team upload. * Rename libraries for 64-bit time_t transition. * Disable building of the PDF documentation due to #1069873. Checksums-Sha1: d1c235bb2a32022e71ac5df11a94bae1e479b669 415072 librdkit-dev_202309.3-4~exp1_i386.deb cf10574a563b2c2ed403bccf08a696c71c845279 101294592 librdkit1t64-dbgsym_202309.3-4~exp1_i386.deb 148a5e63bcddc810347862bdbe67c9b88359c409 5101712 librdkit1t64_202309.3-4~exp1_i386.deb a20ad1d97007135c124a5d6b7137e934f35208ff 1075504 postgresql-16-rdkit-dbgsym_202309.3-4~exp1_i386.deb 77821f3f7130a614e4a667168c5a792a6c830738 505068 postgresql-16-rdkit_202309.3-4~exp1_i386.deb e2cd04fa71f11b19f293db8fbc7cbda0ed4865f0 54287696 python3-rdkit-dbgsym_202309.3-4~exp1_i386.deb c3ab8a0324bdfef89ac1435d182c605e8d6ef76e 4366756 python3-rdkit_202309.3-4~exp1_i386.deb 82cf62eebbb99e1e4c7c487df8fdf8ec4106e04a 13080864 rdkit-data_202309.3-4~exp1_all.deb d18e254c9ba628fbf20dad7b98ee19807b624dd2 6104556 rdkit-doc_202309.3-4~exp1_all.deb f1fc6fc8e6f7eb9a35f91c835c4ea50f5a1d6023 17694 rdkit_202309.3-4~exp1_i386.buildinfo Checksums-Sha256: 7782c56a4feab3df9dfbc116bb297ed6d89926a0fe13c57c8d0687708d1cdb61 415072 librdkit-dev_202309.3-4~exp1_i386.deb fa72642fd5e07661c053d2298a9af44616f4e5eec4304ee526730010567bd075 101294592 librdkit1t64-dbgsym_202309.3-4~exp1_i386.deb c15ab07a19f3f3c9b4fb2d64ce7432c268cff4ee34eedaadd83548591f447346 5101712 librdkit1t64_202309.3-4~exp1_i386.deb d3443082b83f02b25578ce5ec5da552da91a7247dec6f160640fa2356a6c2fc2 1075504 postgresql-16-rdkit-dbgsym_202309.3-4~exp1_i386.deb 7cc961b211c04d8d0075ec0e013ebfba93a402587a09f006ee4c35cb5013f65d 505068 postgresql-16-rdkit_202309.3-4~exp1_i386.deb 5f5ab654a4862c904ca4227899c7cbf66caf723cc91900a54c65e99537bf6619 54287696 python3-rdkit-dbgsym_202309.3-4~exp1_i386.deb 32b414d5ff8fd36ce723e92b30cdbe32102ade745e157b2fa0e4dda10d60b225 4366756 python3-rdkit_202309.3-4~exp1_i386.deb a324cb053ceabcb9470ed260dfbcc41e797eb0132c2bb4bf82b0699c09f3ce1c 13080864 rdkit-data_202309.3-4~exp1_all.deb ddc4e9e664ef05a212ec015ee0a6692bb1a11c1592c106be89d78b203ec337cf 6104556 rdkit-doc_202309.3-4~exp1_all.deb c610272d476eface5db2b1951a67afc05696a80ea83260203b9d3d708e431c0f 17694 rdkit_202309.3-4~exp1_i386.buildinfo Files: 3d615a5fc8d429afce03a78ac4c19c10 415072 libdevel optional librdkit-dev_202309.3-4~exp1_i386.deb 85a56dc6ca19b0102b1fd4406806974c 101294592 debug optional librdkit1t64-dbgsym_202309.3-4~exp1_i386.deb 418f484b31f558cc7dc28acc42cc6427 5101712 libs optional librdkit1t64_202309.3-4~exp1_i386.deb e36d92ae67e4426e835f3441f22feb52 1075504 debug optional postgresql-16-rdkit-dbgsym_202309.3-4~exp1_i386.deb 9165d91dc3bd28c8413146a87fdc72d0 505068 database optional postgresql-16-rdkit_202309.3-4~exp1_i386.deb f81b84375396aae073f4f81a4817ec83 54287696 debug optional python3-rdkit-dbgsym_202309.3-4~exp1_i386.deb 68c1c89781c090ed726b9c1fd0392ea9 4366756 python optional python3-rdkit_202309.3-4~exp1_i386.deb 51d90f7a69856a91ac85ca60e8ab6e5d 13080864 science optional rdkit-data_202309.3-4~exp1_all.deb 0d977a44ae20b5afb240f4698915ab55 6104556 doc optional rdkit-doc_202309.3-4~exp1_all.deb 971c3c06c434895d4431b7de9c1090fb 17694 science optional rdkit_202309.3-4~exp1_i386.buildinfo Sat Apr 27 10:14:47 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_1-25480.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.SxyPlXPs/rdkit_202309.3-4~exp1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.SxyPlXPs/rdkit_202309.3-4~exp1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.SxyPlXPs/rdkit_202309.3-4~exp1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.SxyPlXPs/b1/rdkit_202309.3-4~exp1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.SxyPlXPs/b2/rdkit_202309.3-4~exp1_i386.changes ## close_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer ## command (total time: 3.956s) 1.688s 6 calls xz 1.273s 7 calls diff 0.444s 13 calls cmp 0.443s 13 calls cmp (external) 0.105s 22 calls js-beautify 0.002s 19 calls cmp (internal) ## compare_files (cumulative) (total time: 55.013s) 13.945s 1 call abc.DotChangesFile 13.418s 1 call abc.DebFile 13.344s 2 calls abc.XzFile 11.361s 1 call abc.DebDataTarFile 2.577s 2 calls abc.JavaScriptFile 0.203s 1 call abc.TarFile 0.166s 1 call abc.Md5sumsFile ## container_extract (total time: 4.216s) 2.490s 9480 calls diffoscope.comparators.deb.DebTarContainer 1.688s 6 calls diffoscope.comparators.xz.XzContainer 0.030s 8 calls diffoscope.comparators.deb.DebContainer 0.008s 6 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.656s) 0.656s 12 calls linediff ## has_same_content_as (total time: 0.449s) 0.336s 9 calls abc.DebFile 0.101s 1 call abc.DebDataTarFile 0.005s 2 calls abc.Md5sumsFile 0.004s 1 call abc.TarFile 0.003s 2 calls abc.XzFile 0.000s 3 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 2 calls abc.TextFile 0.000s 1 call abc.DotChangesFile 0.000s 2 calls abc.JavaScriptFile ## main (total time: 17.198s) 17.189s 2 calls outputs 0.009s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 0.763s) 0.761s 1 call html 0.001s 1 call text 0.001s 1 call json ## recognizes (total time: 2.371s) 2.052s 12 calls diffoscope.comparators.binary.FilesystemFile 0.172s 486 calls diffoscope.comparators.debian.DebControlMember 0.091s 566 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.056s 260 calls diffoscope.comparators.utils.archive.ArchiveMember ## specialize (total time: 0.277s) 0.277s 23 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 17.567s CPU time consumed: 17.482s Sat Apr 27 10:15:06 UTC 2024 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Sat Apr 27 10:15:06 UTC 2024 E: rdkit failed to build reproducibly in experimental on i386. Sat Apr 27 10:15:08 UTC 2024 I: Submitting .buildinfo files to external archives: Sat Apr 27 10:15:08 UTC 2024 I: Submitting 20K b1/rdkit_202309.3-4~exp1_i386.buildinfo.asc Sat Apr 27 10:15:11 UTC 2024 I: Submitting 20K b2/rdkit_202309.3-4~exp1_i386.buildinfo.asc Sat Apr 27 10:15:13 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Apr 27 10:15:13 UTC 2024 I: Done submitting .buildinfo files. Sat Apr 27 10:15:13 UTC 2024 I: Removing signed rdkit_202309.3-4~exp1_i386.buildinfo.asc files: removed './b1/rdkit_202309.3-4~exp1_i386.buildinfo.asc' removed './b2/rdkit_202309.3-4~exp1_i386.buildinfo.asc'